Allow display to sleep whilst staying awake

@newmarcel
As per https://github.com/newmarcel/KeepingYouAwake/issues/115, https://github.com/newmarcel/KeepingYouAwake/issues/12 and https://github.com/newmarcel/KeepingYouAwake/issues/25
Would it be possible to integrate your commit https://github.com/newmarcel/KeepingYouAwake/commit/4b0e1688344ba61a8e05802891a2599b9be4f614 into 1.5.2 and allow the display to sleep but the Macbook to stay awake?
As long as caffeinate -i (which prevents Macbook sleep in any situation but allows display sleep) is used and not caffeinate -s (which prevents Macbook sleep only on charger whilst allowing display sleep) there should be no buggines/unexpected behaviour (re: https://github.com/newmarcel/KeepingYouAwake/issues/58 and https://github.com/newmarcel/KeepingYouAwake/issues/67) :)

Came here just to ask the same thing - this option would be invaluable to us!

+1

I was wondering if there had been any movement on this, or plans to include in a 1.5.2 (pre)release?

I just published version 1.5.2 with this feature 😃 https://github.com/newmarcel/KeepingYouAwake/releases/tag/1.5.2
Enjoy, and thanks everyone for pushing for this feature forward 👍


Folder persist after being successfully deleted in blob container

Storage Explorer Version: 1.12.0
Build Number: 20200116.10
Platform/OS: macOS Catalina
Architecture: x86
Regression From:
Bug Description
After I deleted the 'folder', it still persists in the explorer UI. And when I tried to delete again, I saw this error: {
"message": ""failed to perform remove command due to error: nothing found to remove""
}
Steps to Reproduce

delete a folder in a blob container

Expected Experience
The folder will persist. And when you delete again, there will be an error.
Actual Experience

Additional Context

Can you try the failed delete again and share the AzCopy log file with us? You should be able to find the log file in your ~/.azcopy directory. Also what about the remaining blobs in the problematic directory? Can you share their path with us so we can see if AzCopy is handling the paths correctly?

Hi Jason,
The full path is journey-test/adobecom/model_instance/20200112-fatigue-norecency/. Here is what happened in the folder: the deepest folder structure was journey-test/adobecom/model_instance/20200112-fatigue-norecency/email/fatigue/A/training_data/*. After the deletion, the files under training data are gone. But the training_data folder still persists, showing it is a 0B block blob, which is weird.
Here is the AzCopy Command. Sorry I was not able to find the log. Don't see ~/.azcopy.
export AZCOPY_CRED_TYPE=Anonymous;
export AZCOPY_USER_AGENT_PREFIX=Microsoft Azure Storage Explorer, 1.12.0, darwin, ;
./azcopy remove "https://adobecomjourneyaiintstrg.blob.core.windows.net/journey-test/adobecom/model_instance/20200112-fatigue-norecency/?se=2020-03-27T19%3A14%3A53Z&sp=rdl&sv=2018-03-28&sr=c&sig=vZ8E7H0o6QyQEzIQGCpZYS0AG107lhFJUu1htwX0YC4%3D" --recursive
unset AZCOPY_CRED_TYPE;
unset AZCOPY_USER_AGENT_PREFIX;

@kediwu0331 we have investigated the issue and found that the problem was caused by AzCopy intentionally skipping the blobs with metadata hdi_isFolder=True. The metadata is used for representing empty directories due to the fact that Azure Blob Storage doesn't natively support directories. For now, you can go to portal and use the blob viewer there to remove those blobs.

@kediwu0331 I just realized that I may have accidentally deleted some files in your journey-test container 😥. Super sorry about that. Are you able to regenerate the data? Please let us know if there is anything we can do to recover the data.

Hi Jason, could you let me know which files/folders you deleted? Thanks

I selected and deleted the journey-test/adobecom (blob) and see about 601 files getting removed, which due to the same bug, AzCopy goes to delete the files in the adobecom folder. I have the AzCopy log available so I can parse the log to give you a detailed list of files.

Hi Jason, yeah please share the list of files. Thanks!

Here is the list of blobs that I found in the AzCopy log. Each line is the confirmation log message for deleting a single blob item.
accidentally_removed_blobs.txt

Here is a condensed list of files where each line is exactly the relative path for the blob under journey-test/adobecom
condensed_list_of_files.txt

Hi Jason, that's fine. Don't worry about it. The files you deleted are our test models. But for this storage explorer bug, when can it be fixed?

Since we are going to release 1.13.0 mid march and there is no room for us to fit this in it, we are going to push it and relase the fix in 1.14.0.

Let's push the AzCopy team to get this fixed in time for 1.14

For the record, anyone blocked by this can always:

call the Blob APIs yourself to delete the blobs
try to use whatever you originally used to create the blobs to delete them
try removing the hdi_isfolder=true metadata from the blobs (right click -> properties) and then deleting (for this solution, we're not 100% sure what the effects of deleting these blobs will be on the tool that was used to create the blobs, we strongly recommend that you make sure doing this is safe to do in the context of your tool)

Duplicate of https://github.com/microsoft/AzureStorageExplorer/issues/2466


Add support for multiple oidc issuers

It is currently only possible to specify a single oidc issuer. In some environments each microservice has its own oidc issuer. To allow multiple services to authenticate with an openfga instance in such an environment, openfga needs to be modified to accept multiple issuers.

We have another use case for multiple issuers. Our OpenFGA service is deployed in a kubernetes cluster and some services use the issuer kube alias (for internal calls) but we also may have tokens delivered by the authority with the public dns.

Here is a draft PR allowing to specify issuer aliases: #1354 .
The aliases are used as acceptable values for the token issuer validation (iss claim). Note that it still rely on the main issuer jwks for the token validation so it might not fully address the initial use-case.

Release 1.5.1 (https://github.com/openfga/openfga/releases/tag/v1.5.1) includes support for issuer aliases.


Set OS_IDENTITY_API_VERSION=3 in Mitaka jobs

The default value of OS_IDENTITY_API_VERSION is 2.0 in Mitaka devstack,
but V2.0 API of keystone will be deprecated in the future, test against
V3 API of keystone in jobs to keep it ok.

LGTM +1


comp.d should be an effect

A compressor is not a core component and would be better suited in /effect and should also inherit AEffect

It has been moved, but is still defined as a struct.  Converting to a class should be relatively simple.

Changed in 4aa9784


x86: fix pte corruption when setting large regions

We need a copy of the flags field for every PTE we are
updating, we can't just keep OR-ing in the address
field.
Fixes issues seen when setting flags for memory regions
larger than a page.
Signed-off-by: Andrew Boie<EMAIL_ADDRESS>

Codecov Report

Merging #14011 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master   #14011   +/-   ##
=======================================
  Coverage   52.27%   52.27%
=======================================
  Files         307      307
  Lines       45467    45467
  Branches    10525    10525
=======================================
  Hits        23768    23768
  Misses      16901    16901
  Partials     4798     4798

Continue to review full report at Codecov.

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[remove nixpkgs] enable feature for next release

Summary
How was it tested?

Current dependencies on/for this PR:

main

PR #1517   👈

This comment was auto-generated by Graphite.


Hub - allow logged in user to hub to edit profile

Enable edit profile function for user, user allowed to modify picture and any other value

Fixed.


Support RTL language Posts

Checklist

[X] I have read and accepted the contributing guidelines.

Is your feature request related to a problem? Please describe
if the user set the language in the _config.yml to any RTL languages like ar and fr
the HTML layout should automatically change the default test direction to rtl
in all pages like home,page,posts etc.
currently to lokes wrong for Arabic language

Describe the solution you'd like
if the user set the language in the _config.yml to any RTL languages like ar and fr
the HTML layout should automatically change the default test direction to rtl
in all pages like home,page,posts etc.
Describe alternatives you've considered
i have seen this old issue but didn't help
https://github.com/cotes2020/jekyll-theme-chirpy/issues/299
Additional context
No response

i just edited the HTML layout as a bad workaround


Support non-secure flash operations on STM32U5

Hi,
This pull request adds support for non-secure flash operations.
In short, if TrustZone is active (TZEN option bit is 1), it uses secure operations (as before), otherwise it will use non-secure operations.
As a word of caution, this doesn't handle all flash configurations when TrustZone is active. For instance, one can configure watermark-based flash memory protection to designate areas as secure or non-secure. Per section 7.5.1, Table 58., the default configuration when TZEN =1, is that all flash memory is secure. We could expand on this by checking SECWMx_PSTRT and SECWMx_PEND to determine whether one is operating on secure or non-secure flash memory. Though, I figure this might be worthy a discussion.
I tested the existing stm32u5/flash.rs example on a NUCLEO-U575ZI-Q board with TrustZone disabled (TZEN = 0).
Also, I referenced these STM32 examples. Their README's help provide some additional context.
https://github.com/STMicroelectronics/STM32CubeU5/tree/main/Projects/NUCLEO-U575ZI-Q/Examples/FLASH

I'm not sure what's the best way to handle trustzone. There's 3 cases:

trustzone enabled, running in Secure (S) mode => should use the secure registers
trustzone enabled, running in Non-secure (NS) mode => should use the nonsecure registers
trustzone disabled => should use the secure registers (what the current code does. perhaps it doesn't matter?)

so at the very least TZEN=1 doesn't mean we should use the nonsec registers, we might still be running in secure mode.
however, I think instead of detecting this at runtime we should add Cargo features so you can "tell" embassy-stm32 which of the above 3 cases you're building a firmware for. This'd reduce code size, and is unlikely to cause issues because you never want to dynamically run with or without trustzone, the mode is always known at compile time. Perhaps named trustzone-secure, trustzone-nonsecure.

I like the overall approach. That said, I'd like to clarify a few things I've observed:
This is the case that prompted this PR:

trustzone disabled => should use the secure registers (what the current code does. perhaps it doesn't matter?)

With TrustZone disabled (TZEN = 0), I am not able to erase or write to flash using Secure (S) registers. However, I am able to erase and write using Non-secure (NS) registers.
With TrustZone enabled (TZEN = 1), and using the default values for SECWMx_PSTRT and SECWMx_PEND (all flash memory is secure), I can can erase and write to flash using the Secure (S) registers.
In short, the current code works so long as I enable TrustZone (TZEN = 1). To be clear, I'm using the erase and write operations in the stm32u5 flash.rs example for testing.
Also, I need to study the reference manual closer, but aside from using watermark-based secure flash protection, I'm not sure how to configure the these modes:

trustzone enabled, running in Secure (S) mode => should use the secure registers
trustzone enabled, running in Non-secure (NS) mode => should use the nonsecure registers

Specifically, I can designate pages as Secure (S) or Non-secure (NS) using watermark-based protection, but, I'm not familiar with any other way to specify Secure (S) or Non-secure (NS) run modes. I say this mostly because I want to make sure I can test all the cases we're interested in supporting.
Thanks!

This is very helpful context.
I'll update this PR to support Option 1 in a single commit. Then, add support for Option 2 in a follow-on commit.
I'll see if I can update or add an example that demonstrates this as well.
Thanks!

This commit should address option 1: 2fa0bb7
I took a stab at at option 2 with this commit: 0ef0eea
I tested this on a NUCLEO-U575ZI-Q.
For future reference, this was helpful for disabling TrustZone.
With TZEN = 1:
cargo run --release --bin flash --features trustzone-secure // Works (as expected)
cargo run --release --bin flash // Fails (as expected)
With TZEN = 0:
cargo run --release --bin flash // Works (as expected)
cargo run --release --bin flash --features trustzone-secure // Fails (as expected)
I could be missing something here, but I didn't see the value in having two separate features.
Instead, having a single feature, trustzone-secure and then enabling or disabling that feature.
That said, I'm open to whatever features make the most sense here.
Thanks!

Missed adding support secure registers for the clear_all_err().
New commit for option 2: c5119c6


Errors in Manage Palette

I see this error in the manage palette view;

Where would there be a log of this error?  There is nothing in the node-red log.  It does work though.
I am using another Bluetooth node that uses l2ping

I am seeing a lot of these errors in the node-red log
 noble warning: unknown handle 11 disconnected!
I managed to install this node dependency using this solution
https://github.com/noble/node-bluetooth-hci-socket/pull/91#issuecomment-403048810

Should be fixed with 1.2.4


[7.11.24] Add contact list view

Short description

Add list view for the new section "Contacts"
Proposed changes

Add list views for contacts

List view for not archived contacts
List view for archived contacts

Add option to archive, delete, restore and copy contacts
Add test for these four options

Side effects

I think none?
Resolved issues

Fixes: #2952

Pull Request Review Guidelines

Do we need the "copy" functionality? I see the copy option is drawn in the design but we've never talked about it so far I remember 🤔 Of course it doesn't harm anything, but I'm asking for clarifying.

I asked @osmers, and the copy-functionality is still desired as it might make it easier for municipalities to create contacts.

Currently URLs of websites are shown in the column "Phone number". Should we add another column for "Website" although this is not picted in the design?

Oh, good point! I added a website column and I'm showing the phone_number now too :)

I asked @osmers, and the copy-functionality is still desired as it might make it easier for municipalities to create contacts.

Or rather - I'm sure that if we don't add it, we'll have a municipality asking for it and since I don't see any harm in it (please correct me, if I'm overlooking something), I don't see why we shouldn't add it :)

Oh, and it looks like pagination is not working. Could you please add some pagination code to contact_list_view?
To test, just duplicate contacts until you have more than 10. If you then select max 10 entries per page, the paginator should actually limit the number of contacts to that and show two pages total.

I think it would make sense if we would refactor all the other views at some point too, so consistency would not be a problem here imo. But I think it would be ok to either refactor the template in this pr or in another pr :)

@david-venhoff Thank you for all your feedback! I think it should be all applied now (+ a few more changes)

Also looks like the archived contact list is missing the website column. Maybe it would make sense to deduplicate contact_list and contact_list_archived?

Applied :)

@david-venhoff I think this PR is ready for review again. A bit of back information:

I added the check that pois can't be deleted if a contact uses it
I deactivated the buttons to delete a poi
Therefore I had to adapt the test for deleting a poi. As it's not possible to delete a poi anymore that is in use, no ProtectedError will be thrown anymore. Now I'm only checking for a redirect (status 302). However I'm quite unsure, if this is a good practice - I have a feeling it's not. What do you think?

@MizukiTemma could you please check if you think that #3010 is also already resolved by this PR or if you had something different in mind when you created the issue? :)

@JoeyStk Thank you so much for all the work, this is solving #3010 too 😸
One thing to fix is that the success message "Ort "XXX" wurde erfolgreich archiviert" is shown when only a POI which is referenced by a contact is selected and bulk archived.
The POI is anyway not deleted, so I'm fine if this will be fixed in another issue.


preview not displaying

Preview collage  not showing in 1st page .  ImageTk library is broken,
from PIL import Image , ImageTk
 img1 = ImageTk.PhotoImage(Image.open(fullpath("\output\collage1\FinalCollage.png")))
canvas1.create_image(20,20,anchor=NW , image = img1)
Error:
cannot import name 'ImageTk'
python version :  3.9.5
Pillow Version :  8.3.0

Images dont preview inside notebook running inside a child frame.


Experience/DisableCloudOptimizedContent

Experience/DisableCloudOptimizedContent is double-listed.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 6e8ecbe3-ba72-ec44-0591-7f604d50b1e3
Version Independent ID: 9d5ff118-d539-dd6e-ae3e-102392c22287
Content: Policy CSP - Experience - Windows Client Management
Content Source: windows/client-management/mdm/policy-csp-experience.md
Product: w10
Technology: windows
GitHub Login: @ManikaDhiman
Microsoft Alias: dansimp

Hi @KoryKliner, Thanks for pointing this out. I removed the duplicate Experience/DisableCloudOptimizedContent entry from the topic; updates will be live shortly. Thanks again for the feedback!

Resolved in commit https://github.com/MicrosoftDocs/windows-itpro-docs/commit/4efc7e487dddc7fd10fe13f4f536496a359c0a9a . Should be live now.


Wierd compiler bug

Describe your bug here.

\Whenever I tried to compile it for the first time, I was met with this

Command Prompt/Terminal logs (if existing)
source/Achievements.hx:132: characters 30-54 : Warning : `FlxCamera.defaultCameras` is deprecated, use `FlxG.cameras.setDefaultDrawTarget` instead
H:\Wonka DS2\fnf cover mod\PsychEngine-Windows64\Funky Cover Friday V3.0 (SOURCE)\FNF-PsychEngine-main\export\release\windows\obj>setlocal enabledelayedexpansion
Warning: Could not find Visual Studio 2017 VsDevCmd
Missing HXCPP_VARS
Error: Could not automatically setup MSVC

Are you modding a build from source or with Lua?
Source
What is your build target?
Windows
Did you edit anything in this build? If so, mention or summarize your changes.
Nope, it was the first time building it

I have that same problem too

install vs19

Install Visual Studio with choosing Windows SDK and MSVC 142 in installation. I had the same problem.

oh yeah i forgot to update my case installing vsc 2019 worked and i compiled source a few days ago so thx for suggesting that hopefully the other guy has they's fixed

close this issue


n64tool: fix bug in detection of unaligned image sizes

The alignment check in swap_bytes() was still incorrect. This should fix it.

LGTM, thanks for the fix, but I can't merge due to conflicts. Can you rebase on top of trunk and force push?

Ok, is it better now?

Yup!


Exclusion of Inactive, Disabled, Support, and Service Users from Sharing Dialogs

As a normal user of ownCloud Infinite Scale,
I want to only see active and regular users in the sharing dialogs,
So that I can easily find and share with the relevant people without being overwhelmed by inactive, disabled, support, and service accounts.
Acceptance Criteria:

When I access the sharing dialog, I should only see a list of active and regular users.
Any user account that is labeled as 'inactive', 'disabled', 'support', or 'service' or is stored in another realm should not appear in the sharing dialog list.
The search functionality within the sharing dialog should also filter out the aforementioned types of accounts, returning only active and regular users in the search results.

/cc @tbsbdr @wkloucek @micbar @JammingBen

related ticket: https://github.com/owncloud/ocis/issues/8161
Also: Last time a I asked the about this (IIRC @tbsbdr and @micbar were involved), it was agreed that the  "disable user" feature was just meant for being able to prevent user's from signing in. Excluding them from user listings and sharing was specifically not wanted.

Excluding them from user listings and sharing was specifically not wanted.
correct, that is how we wanted it to be for user with the status "login disallowed"


Send data of two inverters in one config

Hi,
I have 2 micro-inverters which report in solarman.
For both I made a config.json which are working, but is it possible, to integrate both inverters into one config.json.
Something like the following?
{
 {
  "name": "TrannergyOne",
  "url": "api.solarmanpv.com",
  "appid": "app",
  "secret": "sec",
  "username"<EMAIL_ADDRESS>  "passhash": "345",
  "stationId": 111,
  "inverterId": 333,
  "loggerId": 555,
  "debug" : false,
  "mqtt":{
    "broker": "<IP_ADDRESS>",
    "port": 1883,
    "topic": "solarmanpv",
    "username": "",
    "password": ""
  }
 },
 {
  "name": "TrannergyTwo",
  "url": "api.solarmanpv.com",
  "appid": "app",
  "secret": "sec",
  "username"<EMAIL_ADDRESS>  "passhash": "345",
  "stationId": 222,
  "inverterId": 444,
  "loggerId": 666,
  "debug" : false,
  "mqtt":{
    "broker": "<IP_ADDRESS>",
    "port": 1883,
    "topic": "solarmanpv",
    "username": "",
    "password": ""
 }
}

Is there a way to let such an example working?
Or how should I run the two configs?
Thank you

Hmm, good one. I'd suggest running two separate instances for now.


[pdpix] Add Support for Windows

Context
Bing is a important collaborator for Demikernel and a path to production. Many Bing services run on Windows. So, having a fully supported Windows port is crucial.
Goal:

Provide a seamless build mechanism for Linux and Windows (based on Makefiles)
Build all Demikernel components (including tests and examples) on Windows
Successfully run all tests Demikernel tests on Windows
Port all LibOSes to Windows

Proposed Solution

[x] Support a seamless build mechanism for Linux and Windows

[x] Split Makefiles for Linux and Windows (https://github.com/demikernel/demikernel/pull/273)
[x] Add Windows Makefiles and ensure that all components build successfully (https://github.com/demikernel/demikernel/pull/309)

[x] Create a hierarchy of subsystems in the Platform Abstraction Layer (https://github.com/demikernel/demikernel/pull/305)
[x] Implement a "Catnap"-like solution for Windows (https://github.com/demikernel/demikernel/pull/314)
[x] Add DPDK support on Windows
[x] Use PAL in all LibOSes

[x] Use PAL in Catnip

[x] Support Bing team to build and test on Windows

The hierarchy of subsystems in the Platform Abstraction Layer should be based on subsystem alone.  In other words, there should be a separate file for each subsystem, with organizing directories only for groupings of subsystems.
For example, for the sockets API, everything related to it should go into the same sockets.rs file.  This file should either be directly in the top level (under pal), or in a Networking directory (if we end up with too many files directly under pal).  There should be no "platform" directories.  The sockets.rs file should contain definitions for everything that is platform specific (constants, function names, structures, whatever).  Inside the file, the definitions should be organized by thing, and not by platform.
I.e.,
#[cfg(target_os = "windows")]
use windows::Win32::Networking::WinSock;

// Socket Address Types
#[cfg(target_os = "linux")]
pub const AF_INET: i32 = libc::AF_INET;
#[cfg(target_os = "windows")]
pub const AF_INET: i32 = WinSock::AF_INET.0 as i32;

// Socket Types
#[cfg(target_os = "linux")]
pub const SOCK_DGRAM: i32 = libc::SOCK_DGRAM;
#[cfg(target_os = "windows")]
pub const SOCK_DGRAM: i32 = WinSock::SOCK_DGRAM as i32;
#[cfg(target_os = "linux")]
pub const SOCK_STREAM: i32 = libc::SOCK_STREAM;
#[cfg(target_os = "windows")]
pub const SOCK_STREAM: i32 = WinSock::SOCK_STREAM as i32;

For this example I alphabetized each thing's platform-specific version by target_os (i.e., the "linux" one before the "windows" one) and to a limited extent the things themselves (i.e., SOCK_DGRAM before SOCK_STREAM).  But the things themselves should obviously be grouped by functionality/applicability (like all socket types together).
Also, if the libc crate is linux specific (as it appears to be from this), then all "use" of it should be platform-specific, as well.

Closing this since Bing clearly has deployed :)


Automated Package Upgrade

:tada: This PR is included in version 25.3.531 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Add ibm-cloud-cognitive to Carbon Devtools

The Carbon devtools () are able to identify components in pages and provide useful information about them. This is not limited to Carbon components themselves, but can also handle components from other related packages (https://github.com/carbon-design-system/devtools/blob/base/packages/web-extension/src/globals/componentList.js), but this does not currently include the C&CS components.
Add the C&CS components to the Carbon devtools, as a useful functional aid for IBM product development teams.
As part of this, we need to figure out the best way to identify C&CS components live in a page. The Carbon, security and Cloud PAL components are identified just by a block class on the main element. Is that sufficient/satisfactory? If so, perhaps we should address the rather overdue question of our own package prefix, which is currently the rather anomalous "exp--", before adding our components to the devtools! Or should we use a different approach, such as some custom tag on the main element?

[ ] Add ibm-cloud-cognitive package to Carbon Devtools repo
[ ] Deliver stable identification mechanism for browser extensions
[ ] Understand and align on maintenance strategy with Devtools contributors


Memory Leak

(Submitted by jrvdboom on Codeplex)
Despite the UndoRoot containing a WeakReference to its root object, memory is still leaked by the _Roots dictionary of the UndoService, because its keys are the same root objects but then strong-referenced. Adding a RemoveRoot method or changing the dictionary to use WeakReference keys can solve the problem.

hi, nice to see this.
I'm not sure that using the ConditionalWeakTable replace the dictonary will be OK
        //private IDictionary<object, UndoRoot> _Roots;
       ConditionalWeakTable <object, UndoRoot> _Roots;
        public UndoService()
        {
             // _Roots = new Dictionary<object, UndoRoot>();
                _Roots = new ConditionalWeakTable<object, UndoRoot>();
        }

But I will using this pacakge, It's wonderful.
Hope it will upgrade soon. I wish the empty changeset issue could be solved too.

This should be fixed in PR #8 and the 2.0 release.
I've converted the UndoService to use weak references for the keys.


Ashleyhx/add hugeint

Also, we should change the title of this PR so it looks better in our release change log.


Submit BioNetGen 2.5.2

id: bionetgen
version: 2.5.2
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BioNetGen/51e87c41eeec5a818410d3a917249a85cde72da1/biosimulators.json
specificationsPatch:
version: 2.5.2
image:
url: ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2
validateImage: true
commitSimulator: true

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

The specifications of your simulator is valid!

The specifications of your simulator is valid!

Summary of tests

Executed 35 test cases

Passed 26 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 9 test cases:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (11.0 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.0 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

sedml.SimulatorProducesLinear2DPlots (7.8 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpplat2whd/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpplat2whd/task.xml.
Running NFsim on 8e7ff88f34cb
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpplat2whd/task.xml -o /tmp/tmpplat2whd/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpplat2whd/task.species -cb -seed<PHONE_NUMBER>
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmpplat2whd/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 0.913542s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpplat2whd/task.species
Read 0 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.28 s.
Finished processing file /tmp/tmpplat2whd/task.bngl.
CPU TIME: total 5.77 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (10.4 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmp5gc0bcda/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmp5gc0bcda/task.xml.
Running NFsim on 539fa4d1fc33
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp5gc0bcda/task.xml -o /tmp/tmp5gc0bcda/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmp5gc0bcda/task.species -seed 795663570 -cb
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with: 795663570
reading xml file (/tmp/tmp5gc0bcda/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 3.56203s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmp5gc0bcda/task.species
Read 4 unique species of 75 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 3.92 s.
Finished processing file /tmp/tmp5gc0bcda/task.bngl.
CPU TIME: total 8.31 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (7.9 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpu7bbfvj6/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpu7bbfvj6/task.xml.
Running NFsim on d3f29cf17e8d
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpu7bbfvj6/task.xml -o /tmp/tmpu7bbfvj6/task.gdat -sim 100 -oSteps 100 -cb -ss /tmp/tmpu7bbfvj6/task.species -seed<PHONE_NUMBER>
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmpu7bbfvj6/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 0.932214s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpu7bbfvj6/task.species
Read 1 unique species of 74 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.31 s.
Finished processing file /tmp/tmpu7bbfvj6/task.bngl.
CPU TIME: total 5.83 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (10.2 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmprexly4jw/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmprexly4jw/task.xml.
Running NFsim on 1332acbb4f3b
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmprexly4jw/task.xml -o /tmp/tmprexly4jw/task.gdat -sim 100 -oSteps 100 -seed<PHONE_NUMBER> -ss /tmp/tmprexly4jw/task.species -cb
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmprexly4jw/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 3.16551s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmprexly4jw/task.species
Read 9 unique species of 78 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 3.54 s.
Finished processing file /tmp/tmprexly4jw/task.bngl.
CPU TIME: total 8.04 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (12.5 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (2):
      plot_0: 2 curves
      plot_1: 1 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpw02cb8g_/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpw02cb8g_/task.xml.
Running NFsim on 8135a10f9025
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpw02cb8g_/task.xml -o /tmp/tmpw02cb8g_/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpw02cb8g_/task.species -cb -seed 909892705
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with: 909892705
reading xml file (/tmp/tmpw02cb8g_/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 5.62757s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpw02cb8g_/task.species
Read 4 unique species of 75 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 6.00 s.
Finished processing file /tmp/tmpw02cb8g_/task.bngl.
CPU TIME: total 10.45 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (1.8 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Reports (1):
      report: 3 data sets

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
The initial time of a network free simulation (KISAO_0000263) must be 0.

Summary of tests

Executed 35 test cases

Passed 26 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 9 test cases:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (11.0 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.0 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

sedml.SimulatorProducesLinear2DPlots (7.8 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpplat2whd/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpplat2whd/task.xml.
Running NFsim on 8e7ff88f34cb
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpplat2whd/task.xml -o /tmp/tmpplat2whd/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpplat2whd/task.species -cb -seed<PHONE_NUMBER>
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmpplat2whd/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 0.913542s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpplat2whd/task.species
Read 0 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.28 s.
Finished processing file /tmp/tmpplat2whd/task.bngl.
CPU TIME: total 5.77 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (10.4 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmp5gc0bcda/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmp5gc0bcda/task.xml.
Running NFsim on 539fa4d1fc33
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp5gc0bcda/task.xml -o /tmp/tmp5gc0bcda/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmp5gc0bcda/task.species -seed 795663570 -cb
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with: 795663570
reading xml file (/tmp/tmp5gc0bcda/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 3.56203s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmp5gc0bcda/task.species
Read 4 unique species of 75 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 3.92 s.
Finished processing file /tmp/tmp5gc0bcda/task.bngl.
CPU TIME: total 8.31 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (7.9 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpu7bbfvj6/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpu7bbfvj6/task.xml.
Running NFsim on d3f29cf17e8d
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpu7bbfvj6/task.xml -o /tmp/tmpu7bbfvj6/task.gdat -sim 100 -oSteps 100 -cb -ss /tmp/tmpu7bbfvj6/task.species -seed<PHONE_NUMBER>
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmpu7bbfvj6/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 0.932214s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpu7bbfvj6/task.species
Read 1 unique species of 74 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.31 s.
Finished processing file /tmp/tmpu7bbfvj6/task.bngl.
CPU TIME: total 5.83 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (10.2 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmprexly4jw/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmprexly4jw/task.xml.
Running NFsim on 1332acbb4f3b
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmprexly4jw/task.xml -o /tmp/tmprexly4jw/task.gdat -sim 100 -oSteps 100 -seed<PHONE_NUMBER> -ss /tmp/tmprexly4jw/task.species -cb
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmprexly4jw/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 3.16551s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmprexly4jw/task.species
Read 9 unique species of 78 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 3.54 s.
Finished processing file /tmp/tmprexly4jw/task.bngl.
CPU TIME: total 8.04 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (12.5 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (2):
      plot_0: 2 curves
      plot_1: 1 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpw02cb8g_/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpw02cb8g_/task.xml.
Running NFsim on 8135a10f9025
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpw02cb8g_/task.xml -o /tmp/tmpw02cb8g_/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpw02cb8g_/task.species -cb -seed 909892705
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with: 909892705
reading xml file (/tmp/tmpw02cb8g_/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 5.62757s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpw02cb8g_/task.species
Read 4 unique species of 75 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 6.00 s.
Finished processing file /tmp/tmpw02cb8g_/task.bngl.
CPU TIME: total 10.45 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (1.8 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Reports (1):
      report: 3 data sets

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
The initial time of a network free simulation (KISAO_0000263) must be 0.

The image for your simulator is valid!

The image for your simulator is valid!

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job is available here.

The specifications of your simulator is valid!

The specifications of your simulator is valid!

Summary of tests

Executed 35 test cases

Passed 26 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 9 test cases:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (10.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.7 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

sedml.SimulatorProducesLinear2DPlots (10.9 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmp71tebu76/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmp71tebu76/task.xml.
Running NFsim on 4670f4541e83
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp71tebu76/task.xml -o /tmp/tmp71tebu76/task.gdat -sim 100 -oSteps 100 -seed<PHONE_NUMBER> -cb -ss /tmp/tmp71tebu76/task.species
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmp71tebu76/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 1.09648s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmp71tebu76/task.species
Read 0 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.68 s.
Finished processing file /tmp/tmp71tebu76/task.bngl.
CPU TIME: total 7.74 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (10.8 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpvcz2dw_z/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpvcz2dw_z/task.xml.
Running NFsim on 3badd09216ff
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpvcz2dw_z/task.xml -o /tmp/tmpvcz2dw_z/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpvcz2dw_z/task.species -cb -seed 72033610
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with: 72033610
reading xml file (/tmp/tmpvcz2dw_z/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 1.06919s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpvcz2dw_z/task.species
Read 1 unique species of 74 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.67 s.
Finished processing file /tmp/tmpvcz2dw_z/task.bngl.
CPU TIME: total 7.59 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (14.9 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpek28t6q7/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpek28t6q7/task.xml.
Running NFsim on 2c8ce9364d40
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpek28t6q7/task.xml -o /tmp/tmpek28t6q7/task.gdat -sim 100 -oSteps 100 -seed 193300752 -cb -ss /tmp/tmpek28t6q7/task.species
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with: 193300752
reading xml file (/tmp/tmpek28t6q7/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 5.13532s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpek28t6q7/task.species
Read 4 unique species of 74 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 5.78 s.
Finished processing file /tmp/tmpek28t6q7/task.bngl.
CPU TIME: total 11.68 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (11.2 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmp8cqq0b1l/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmp8cqq0b1l/task.xml.
Running NFsim on 93e146429b92
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp8cqq0b1l/task.xml -o /tmp/tmp8cqq0b1l/task.gdat -sim 100 -oSteps 100 -cb -seed 109440741 -ss /tmp/tmp8cqq0b1l/task.species
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with: 109440741
reading xml file (/tmp/tmp8cqq0b1l/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 1.11805s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmp8cqq0b1l/task.species
Read 0 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.69 s.
Finished processing file /tmp/tmp8cqq0b1l/task.bngl.
CPU TIME: total 7.81 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (16.2 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (2):
      plot_0: 2 curves
      plot_1: 1 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpz_xo5cuu/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpz_xo5cuu/task.xml.
Running NFsim on cdb9fea18a12
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpz_xo5cuu/task.xml -o /tmp/tmpz_xo5cuu/task.gdat -sim 100 -oSteps 100 -cb -ss /tmp/tmpz_xo5cuu/task.species -seed 497220219
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with: 497220219
reading xml file (/tmp/tmpz_xo5cuu/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 6.3467s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpz_xo5cuu/task.species
Read 4 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 6.92 s.
Finished processing file /tmp/tmpz_xo5cuu/task.bngl.
CPU TIME: total 13.01 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Reports (1):
      report: 3 data sets

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
The initial time of a network free simulation (KISAO_0000263) must be 0.

Summary of tests

Executed 35 test cases

Passed 26 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 9 test cases:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (10.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.7 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

sedml.SimulatorProducesLinear2DPlots (10.9 s)
Test that a simulator produces linear 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmp71tebu76/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmp71tebu76/task.xml.
Running NFsim on 4670f4541e83
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp71tebu76/task.xml -o /tmp/tmp71tebu76/task.gdat -sim 100 -oSteps 100 -seed<PHONE_NUMBER> -cb -ss /tmp/tmp71tebu76/task.species
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with:<PHONE_NUMBER>
reading xml file (/tmp/tmp71tebu76/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 1.09648s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmp71tebu76/task.species
Read 0 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.68 s.
Finished processing file /tmp/tmp71tebu76/task.bngl.
CPU TIME: total 7.74 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (10.8 s)
Test that a simulator produces linear 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpvcz2dw_z/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpvcz2dw_z/task.xml.
Running NFsim on 3badd09216ff
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpvcz2dw_z/task.xml -o /tmp/tmpvcz2dw_z/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpvcz2dw_z/task.species -cb -seed 72033610
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with: 72033610
reading xml file (/tmp/tmpvcz2dw_z/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 1.06919s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpvcz2dw_z/task.species
Read 1 unique species of 74 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.67 s.
Finished processing file /tmp/tmpvcz2dw_z/task.bngl.
CPU TIME: total 7.59 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (14.9 s)
Test that a simulator produces logarithmic 2D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpek28t6q7/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpek28t6q7/task.xml.
Running NFsim on 2c8ce9364d40
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpek28t6q7/task.xml -o /tmp/tmpek28t6q7/task.gdat -sim 100 -oSteps 100 -seed 193300752 -cb -ss /tmp/tmpek28t6q7/task.species
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with: 193300752
reading xml file (/tmp/tmpek28t6q7/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 5.13532s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpek28t6q7/task.species
Read 4 unique species of 74 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 5.78 s.
Finished processing file /tmp/tmpek28t6q7/task.bngl.
CPU TIME: total 11.68 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (11.2 s)
Test that a simulator produces logarithmic 3D plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (1):
      plot_0: 3 surfaces

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmp8cqq0b1l/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmp8cqq0b1l/task.xml.
Running NFsim on 93e146429b92
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp8cqq0b1l/task.xml -o /tmp/tmp8cqq0b1l/task.gdat -sim 100 -oSteps 100 -cb -seed 109440741 -ss /tmp/tmp8cqq0b1l/task.species
[simulation PID is: 15]
starting NFsim v1.12.1...

Seeding random number generator with: 109440741
reading xml file (/tmp/tmp8cqq0b1l/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 1.11805s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmp8cqq0b1l/task.species
Read 0 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 1.69 s.
Finished processing file /tmp/tmp8cqq0b1l/task.bngl.
CPU TIME: total 7.81 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (16.2 s)
Test that a simulator produces multiple plots
Warnings:
Simulator did not produce plots

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Plots (2):
      plot_0: 2 curves
      plot_1: 1 curves

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
BioNetGen version 2.5.2
Reading from file /tmp/tmpz_xo5cuu/task.bngl (level 0)
Read 73 parameters.
Read 74 molecule types.
Read 75 species.
Read 178 observable(s).
Read 9 functions.
Read 2339 reaction rule(s).
ACTION: simulate( method=>"nf" )
NetworkFree simulation using nf
ACTION: simulate_nf( )
Wrote model in xml format to /tmp/tmpz_xo5cuu/task.xml.
Running NFsim on cdb9fea18a12
full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpz_xo5cuu/task.xml -o /tmp/tmpz_xo5cuu/task.gdat -sim 100 -oSteps 100 -cb -ss /tmp/tmpz_xo5cuu/task.species -seed 497220219
[simulation PID is: 14]
starting NFsim v1.12.1...

Seeding random number generator with: 497220219
reading xml file (/tmp/tmpz_xo5cuu/task.xml)
	[-------]
preparing simulation...

Equilibrating for :0s.  Please wait.

simulating system for: 1.000000e+02 second(s).

  Total CPU time: 6.3467s

SpeciesLabel max molecule threshold set to 20.
WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
readNFspecies::Reading from file /tmp/tmpz_xo5cuu/task.species
Read 4 unique species of 73 total.
SpeciesLabel max molecule threshold set to 0.
  (all species will be labeled with the Auto method)
CPU TIME: simulate 6.92 s.
Finished processing file /tmp/tmpz_xo5cuu/task.bngl.
CPU TIME: total 13.01 s.
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
/usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.0 s)
Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  Dolan2015.sedml:
    Tasks (1):
      simulation_1
    Reports (1):
      report: 3 data sets

Executing SED-ML file 0: Dolan2015.sedml
  Found 1 tasks
    simulation_1
  Executing task 1: simulation_1
/usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
The initial time of a network free simulation (KISAO_0000263) must be 0.

The image for your simulator is valid!

The image for your simulator is valid!

The validation/submission of your simulator failed.
- 500 Server Error: Internal Server Error for url: https://api.biosimulators.org/simulators

The complete log of your validation/submission job, including further information about the failure, is available here.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

The validation/submission of your simulator failed.
- 500 Server Error: Internal Server Error for url: https://api.biosimulators.org/simulators

The complete log of your validation/submission job, including further information about the failure, is available here.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Looks like there was an error with the API. I manually submitted the specs to the database.

Looks like there was an error with the API. I manually submitted the specs to the database.


Fix for combo box issue on retina display

This should fix the issue, the combobox is now set to the default height. Not sure exactly how to compile this into an OSX binary to test it fully.

It look extremely bad.


Fix multiline import statements (proposal for issue #8)

Hi @myint. Thank you very much for creating this awesome project.
This PR is my proposal on how to tackle #8. I hope you find it relevant.
It still skips difficult scenarios like lines joined by a semicolon, inline try-catch, comments and etc, but I think tackling everything would increase the complexity of the code to an undesired level.

Coverage increased (+0.01%) to 99.335% when pulling d86860d5a5f2e17bab85f017fd7a9ce5a72b254f on abravalheri:fix-multiline-from-imports into 095161e50fbe36c0077b894674b7128da2061b6d on myint:master.

Coverage increased (+0.01%) to 99.335% when pulling d86860d5a5f2e17bab85f017fd7a9ce5a72b254f on abravalheri:fix-multiline-from-imports into 095161e50fbe36c0077b894674b7128da2061b6d on myint:master.

Thanks! I'll have to review this in more detail when I get a chance.

@myint Please review this MR and merge whenever possible. This should be fixed.


[Shadowbane Inquisition] bug fix and test CRP

Submission Checklist
Required

[ x ] The pull request title clearly contains the name of the sheet I am editing.
[ x ] The pull request title clearly states the type of change I am submitting (New Sheet/New Feature/Bugfix/etc.).
[ x ] The pull request makes changes to files in only one sub-folder.
[ x ] The pull request does not contain changes to any json files in the translations folder (translation.json is permitted)

New Sheet Details

The name of this game is: <   >  (i.e. Dungeons & Dragons 5th Edition, The Dresden Files RPG)

The publisher of this game is: <   > (i.e. Wizards of the Coast, Evil Hat)

The name of this game system/family is: <   > (i.e. Dungeons & Dragons, FATE)

[ ] I have followed the Character Sheets Standards when building this sheet.

[ ] This sheet has been made on behalf of, or by, the game's publisher.
[ ] This game is not a traditionally published game, but a copy of the game rules can be purchased/downloaded/found at: <   >
[ ] This sheet is for an unofficial fan game, modification to an existing game, or a homebrew system.

Changes / Description
fixed the typo that caused bad calculations
test trial of a simple CRP

Character Sheet Info Roll20 Internal Use only.