ZipInputStream not finding next entry if entry is a folder with a Data Descriptor Still Not Fixed

I believe this issue is still not fixed (tested in 2.9.0).   The attached simple example of writing a zip archive with just two directories using ZipOutputStream and then reading with ZipInputStream fails to read the second entry.
The offending code seems to be in ZipInputStream.read(byte[], int, int) lines 155-157:
    if (localFileHeader.isDirectory()) {       return -1;     }
Since this stops reading before endOfCompressedDataRecord() can be called, and subsequently read the data descriptor block.   Reading the next entry then silently fails because the signature is for a data descriptor and not a local file header.
Zip4jDirectoryDataDescriptorBug.zip
Originally posted by @mbach979 in https://github.com/srikanth-lingala/zip4j/issues/309#issuecomment-910485641

Thanks for your analysis and also the sample code to test the issue. It really helped. I fixed the issue and I will include the fix in next release.

Fixed in v2.9.1 released today.


python310Packages.hahomematic: 2023.1.4 -> 2023.1.5

Diff: https://github.com/danielperna84/hahomematic/compare/refs/tags/2023.1.4...2023.1.5
Changelog: https://github.com/danielperna84/hahomematic/releases/tag/2023.1.5
Description of changes

Things done

Built on platform(s)

[ ] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
23.05 Release Notes (or backporting 22.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[ ] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 211793 run on x86_64-linux 1

2 packages built:

python310Packages.hahomematic
python311Packages.hahomematic


stm32f746g-disco:lvgl, fb, nxdemo, nxterm  "arm_hardfault: PANIC!!! Hard fault:"

Among the stm32f746g-disco configurations, only the "stm32f746-disco:nsh" works as expected, and nsh> prompt comes through the usart6 terminal. For all others; stm32f746g-disco:lvgl, fb, nxdemo, nxterm the usart6 terminal does not respond, and from acm0 terminal the "arm_hardfault: PANIC !!! Hard fault:" response is received. Am I making a mistake or is this a bug?

Hi TA1DB, it is not a BUG. The other configs are using UART1 instead UART6. Thank you for reporting it, I will submit a fix!

Hi Alan, UART6 seems like a better choice for the default serial port as it is connected to the ST-link virtual COM. Connecting an external UART interface can be annoying if the board already has one built-in.

Hi Raiden, yes I was looking the schematic and datasheet when I saw your message here. I will move nsh config from USART6 to USART1 and update the README.

Hi @acassis , thanks for your prompt and helpful answer.
My choice would be UART6 because we used UART6 in my other linux trials, so I could continue my nuttx trials without changing pins, but I respect your explanations and preferences.
Could I somehow easily choose UART6 instead of UART1 in my configuration with "make menuconfig" or in any way? I am new to Nuttx; can you give me information about this possibility.

Hi TA1DB, yes all you need to do it:
$ make menuconfig
System Type  --->
STM32 Peripheral Support  --->
[*] USART6
Device Drivers  --->
[*] Serial Driver Support  --->
Serial console (USART1)  --->
(X) USART6
It is important to keep it on USART1 because it will make the live of other users more easy. I just submitted the PR #1644 to fix it.

Hi @acassis
I have to re-open the issue because my main problem was related to receiving
"arm_hardfault: PANIC!!! Hard fault:""
instead of a nsh> prompt.
After this revision now the properly working :nsh config moved from USART6 to USART1, it works well as it was working previously but the other configs (lvgl, fb, nxdemo..) respond with "arm_hardfault: PANIC!!! Hard fault:" after reset on USART1 (ttyACM0 in my case).

Hi @TA1DB,
I don't have this board here to help you with debugging. Probably it could be something easy to fix, like when the stack size defined is too small. BTW, you can try to verify what is causing the hardfault, please take a look in this documentation:
https://cwiki.apache.org/confluence/display/NUTTX/Analyzing+Cortex-M+Hardfaults
If you have other LVGL supported board, like the STM32F429I-Disco, please try it. I have this board here, case you face similar issue.

I have done some experiments to resolve the issue with my limited knowledge and limited experience about Nuttx. Stm32f746g-disco: nsh building and running, no problem! I canfigured this. Then I activated lvgl with "make menuconfig". It compiled and worked again without any problems. When I activate the "lvgl demo" in examples then the source code is not compiled, "make" returns with the following error messages:
`In file included from ./tp.c:57:0:
./tp.h:63:4: error: #error "Input device support is not enabled (CONFIG_INPUT)"
error "Input device support is not enabled (CONFIG_INPUT)"
^

ERROR: arm-none-eabi-gcc failed: 1
command: arm-none-eabi-gcc -MT ./tp.home.user.nuttxspace.apps.examples.lvgldemo.o  -M '-fno-builtin' '-Wall' '-Wstrict-prototypes' '-Wshadow' '-Wundef' '-g' '-mcpu=cortex-m7' '-mthumb' '-mfloat-abi=soft' '-isystem' '/home/user/nuttxspace/nuttx/include' '-D__KERNEL__' '-pipe' '-I' '/home/user/nuttxspace/apps/graphics/lvgl' '-I' '/home/user/nuttxspace/apps/graphics/lvgl/lvgl' '-I' '/home/user/nuttxspace/apps/include' '-DLV_LVGL_H_INCLUDE_SIMPLE' ./tp.c
/home/user/nuttxspace/apps/Application.mk:228: recipe for target '.depend' failed
make[2]: *** [.depend] Error 1
make[2]: Leaving directory '/home/user/nuttxspace/apps/examples/lvgldemo'
Makefile:55: recipe for target '/home/user/nuttxspace/apps/examples/lvgldemo_depend' failed
make[1]: *** [/home/murat/nuttxspace/apps/examples/lvgldemo_depend] Error 2
make[1]: Leaving directory '/home/murat/nuttxspace/apps'
tools/Makefile.unix:446: recipe for target 'pass2dep' failed
make: *** [pass2dep] Error 2
`

Hi Murat,
in this case the build error is reporting the issue to you:
#error "Input device support is not enabled (CONFIG_INPUT)" error "Input device support is not enabled (CONFIG_INPUT)"
The LVGL demo needs an Input device (i.e. a TouchScreen driver or a Mouse) to work. You could see in the lvgl/defconfig what is enabled and try to enable it too.

Hello Alan.
By this way I could build a working .bin file together with some "examples" including lvgl as well. nsh> promt comes and if I enter ? or help I see the list of builtin apps. However if I start lvgl or tc then I get the same "arm_hardfault: PANIC!!! Hard fault:" response. On the other hand the "Hello" works as expected.

Hi Murat, the functions up_fbinitialize() and up_fbgetvplane() are here:
boards/arm/stm32f7/stm32f746g-disco/src/stm32_lcd.c:int up_fbinitialize(int display)
But this file depends on CONFIG_STM32F7_LTDC enabled in the menuconfig to be compiled:
ifeq ($(CONFIG_STM32F7_LTDC),y)
CSRCS += stm32_lcd.c
endif
So, try to enable it and see what you get.

Hi, Alan, now the compiler complains about the ltdc bubber size . How can I enter a good buffer size? Can you recommend a good value to satisfy the compiler :)
`make[2]: Leaving directory '/home/murat/nuttxspace/nuttx/boards/arm/stm32f7/stm32f746g-disco/src'
chip/stm32_ltdc.c:293:4: error: #error "STM32_LTDC_BUFFER_SIZE not large enough for frame buffers"
error "STM32_LTDC_BUFFER_SIZE not large enough for frame buffers"
ERROR: arm-none-eabi-gcc failed: 1
command: arm-none-eabi-gcc -M '-fno-builtin' '-Wall' '-Wstrict-prototypes' '-Wshadow' '-Wundef' '-g' '-mcpu=cortex-m7' '-mthumb' '-mfloat-abi=soft' '-isystem' '/home/murat/nuttxspace/nuttx/include' '-D__KERNEL__' '-pipe' '-I' '/home/murat/nuttxspace/nuttx/arch/arm/src/chip' '-I' '/home/murat/nuttxspace/nuttx/arch/arm/src/common' '-I' '/home/murat/nuttxspace/nuttx/arch/arm/src/armv7-m' '-I' '/home/murat/nuttxspace/nuttx/sched' '-D__KERNEL__' chip/stm32_ltdc.c
Makefile:199: recipe for target '.depend' failed
make[1]: *** [.depend] Error 1
make[1]: Leaving directory '/home/murat/nuttxspace/nuttx/arch/arm/src'
tools/Makefile.unix:446: recipe for target 'pass2dep' failed
make: *** [pass2dep] Error 2
`

For stm32f429i-disco it is about 300KiB, try to use the same value:
CONFIG_STM32_LTDC_FB_SIZE=307200

For stm32f429i-disco it is about 300KiB, try to use the same value:
CONFIG_STM32_LTDC_FB_SIZE=307200

This is the internal SRAM:
CONFIG_RAM_SIZE=114688
CONFIG_RAM_START=0x20000000
The internal SRAM is insufficient to support frambebuffers. There are
two framebuffers in the fb configuration that lie in external RAM:
CONFIG_STM32_DMA2D_FB_BASE=0xD07B5000
CONFIG_STM32_DMA2D_FB_SIZE=307200
CONFIG_STM32_LTDC_FB_BASE=0xD076A000
CONFIG_STM32_LTDC_FB_SIZE=307200
The address is determined by which FMC chip select you use.  The
framebuffers are excluded from the heap via:
CONFIG_HEAP2_BASE=0xD0000000
CONFIG_HEAP2_SIZE=7774208
Just setting the framebuffer size without initializing and managing the
external memory would not work.

Just setting the framebuffer size without initializing and managing the external memory would not work.

Yes. From my previous experince I remember that stm32f746g-disco board's display resolution 448x272 pixel 3x8 bit wide, here in this application there is the necessary informaton:
Creating a graphical application with LTDC page 33

I think the 448x272 in that PDF is just for the example image they're displaying; the display's actual dimensions are 480x272.

Framebuffer size is 480x272x3 = 391680 bytes
Framebuffer start address (can be) 0xC0000000
`In file included from chip/stm32_ltdc.c:58:0:
chip/stm32_ltdc.c: In function 'stm32_ltdc_lclutenable':
chip/stm32_ltdc.c:2018:43: error: 'struct stm32_ltdc_s' has no member named 'oinfo'
regval = getreg32(stm32_cr_layer_t[layer->oinfo.overlay]);
^
/home/murat/nuttxspace/nuttx/arch/arm/src/common/arm_arch.h:43:55: note: in definition of macro 'getreg32'
define getreg32(a)          (*(volatile uint32_t *)(a))
                                                   ^

chip/stm32_ltdc.c:2033:42: error: 'struct stm32_ltdc_s' has no member named 'oinfo'
putreg32(regval, stm32_cr_layer_t[layer->oinfo.overlay]);
^
/home/murat/nuttxspace/nuttx/arch/arm/src/common/arm_arch.h:44:55: note: in definition of macro 'putreg32'
define putreg32(v,a)        (*(volatile uint32_t *)(a) = (v))
                                                   ^

chip/stm32_ltdc.c: In function 'stm32_ltdc_lputclut':
chip/stm32_ltdc.c:2080:50: error: 'struct stm32_ltdc_s' has no member named 'oinfo'
putreg32(regval, stm32_clutwr_layer_t[layer->oinfo.overlay]);
^
/home/murat/nuttxspace/nuttx/arch/arm/src/common/arm_arch.h:44:55: note: in definition of macro 'putreg32'
define putreg32(v,a)        (*(volatile uint32_t *)(a) = (v))
                                                   ^

Makefile:154: recipe for target 'stm32_ltdc.o' failed
make[1]: *** [stm32_ltdc.o] Error 1
make[1]: Leaving directory '/home/murat/nuttxspace/nuttx/arch/arm/src'
tools/LibTargets.mk:161: recipe for target 'arch/arm/src/libarch.a' failed
make: *** [arch/arm/src/libarch.a] Error 2`

Hi Murat,
please take a look in the source could to find the root of the issue:
#ifdef CONFIG_FB_OVERLAY
struct   fb_overlayinfo_s oinfo;            /* Overlay info */
#endif
"oinfo" only will exist if CONFIG_FB_OVERLAY is selected in the menuconfig.

Hi Alan,
As I've said in linkedin messaging I still get the "arm_hardfault: PANIC!!! Hard fault:" error at the end even if I solve the particular errors in compiling the applications/examples. My knowledge and experience in Nuttx is not yet sufficient to find a permanent solution to this issue (I want to improve it). I hope and look forward you get your stm32f746g-disco board soon and be able to resolve the issue. Thanks BR.

just a note: the same problem happens in version 9.0.0 as well

Hi Murat, don't worry, my board should arrive this week and by the weekend I will try to help you. BTW, if you get a F429I-Disco you can play with LVGL without these issues, but keep in mind that this board it not so complete like the F746G0-Disco

Hi @acassis , did you receive your board ?
Please note there is a very similar issue here Hard fault in STM32H7 protected mode, myabe if you can resolve this issue our solution may help tehm tehere.
In the meantime I already played with lvgl on F429I-Disco but it's display is very small and the board has much less features, therefore not only me, I beleive many others will thank to you for your help. Regards, Murat.

Hi Everybody,
Upon suggestion of Jonathan Gonzaga in this discussion I checked my arm-none-eabi installation, surprisingly found that there was 2 installs, one from 2015 Ubuntu's default toollchain and the other one was my new 2020 installation, I just simply did apt-get uninstall gcc-arm-none-eabi then my new Nuttx builds started working normally. Lvgldemo also works fine. I am closing this issue. Thanks.


Amplify iOS Roadmap/General Availability

The docs say Amplify iOS is in preview mode and not intended for production usage at this time. Is there a target date for that to change to GA?
Latest versions of everything if you are interested.

Sorry to chase but could we get an answer. And apologies if I sound like I am ranting but I haven't seen much progress in the last 2 months.
There are so many problems currently in different parts of the framework that I am spending more time implementing workarounds than using basic functionality that is documented but not functional.

analytics - don't see data
storage - can't upload/download
API/datastore - don't even want to start thinking about how many sleepless nights I had trying to troubleshoot and workaround object connections that don't show up in DynamoDB.
building on a device - no longer possible

It takes an awful amount of time to get the attention of the team when an issue related to core functionality is reported. At least a rough timeline of when we can expect to go out of preview mode would really help. At this point I am really contemplating going back to the old SDK because that was A LOT more stable and usable ... or even using a different framework all together.
I and probably many other developers need to understand when can we look at launching our applications to production. It's not fun when you have a concept in mind and somebody beats you to releasing it to the app store, been there, done that.

+1

@amuresia Apologies for your frustration. We are working diligently to get the Amplify iOS libraries to GA as soon as possible. Can you share any log data around the failures you are experiencing? Also, are you using the published pods or the GitHub repository? There are a few issues we are actively working on that might relate to what you are seeing here, but without more details/logs it's hard to know what you are running into:

Analytics: https://github.com/aws-amplify/amplify-ios/issues/270
Storage: https://github.com/aws-amplify/amplify-ios/issues/339
DatasStore/API: https://github.com/aws-amplify/amplify-ios/issues/340

Particularly here: https://github.com/aws-amplify/amplify-ios/issues/340#issuecomment-592726629

Unsure what you mean by this one, can you clarify?

Apologies you feel like responses are slow, we have a weekly on-call rotation that both addresses issues full time on this repo and the SDK and we try to answer them as quickly as possible as we iterate. Do you have a particular issue that you've posted you can point me to that has not been answered yet?
We will launch the GA of the Amplify iOS libraries this year. We are shooting for GA around Q2-Q3 timeline, but actively working on it to get there as soon as we complete functionality and are sure it is as stable and bug free as possible. We launched preview so that we can get customers testing/trying out our implementation and gather feedback so that we don't build just what we think but actively participate in the open source community. Also, just to be clear, the existing AWS Mobile SDK for iOS is GA and production ready. However, it is our goal to make the Amplify iOS libraries the go-to entry point for mobile apps (as with JavaScript)...I'd really like to help address your issues and make sure we are at least tracking the appropriate issues (listed above) or make sure we have anything else you are experiencing tracked. So, please let me know if these above are related, or if you are running into anything else. We will definitely update these issues as we publish/update the codebase/pods and please let me know some clarify on the last bullet there.
cc @drochetti for DataStore/Analytics, @lawmicha for Storage

@jeffla @Ricardo1980 @amuresia @jtmorris314 Amplify for iOS just went GA! The v1.0.0 is officially out.
We also have a new step-by-step tutorial using Amplify.DataStore.
Last but not least, we launched a Discord community, feel free to join us there and share more about your use-cases and experience: https://discord.gg/Px5YVfQ


how use the isKubernetes diagnostic option

Hello!
I'm trying to understand what the isKubernetes property on the DiagnosticsOptions interface does - if/how to use it... I couldn't find anything helpful here or in the language-server repo - can anyone provide some insight / point me to somewhere I can learn?
thanks in advance!
/Ole

In order to understand, it’s important to understand yaml-language-server consists of 2 parts:

The YAML language service
The YAML language server

monaco-yaml only uses the language service part. From what I can tell, the isKubernetes option uses slightly different algorithms for handling oneOf schemas. These are supposed to handle Kubernetes resources, which basically have to adhere to one of many sub schemas, in a more user friendly manner.
For completeness sake I’ll also explain the language server part. This part turns a JSON schema URI of 'kubernetes' to 'https://raw.githubusercontent.com/yannh/kubernetes-json-schema/master/v1.20.5-standalone-strict/all.json'. This is a big JSON schema which defines many Kubernetes related resources. Unfortunately this JSON schema doesn’t appear to work with monaco-yaml our of the box.
Beware I might be wrong about some things. I based this on some inspection I did on yaml-language-server myself.
I hope this helps. :)

Thanks @remcohaszing for taking your time to answer - this definitely helps!


make ripple effect for scrollable tab tar

like here https://github.com/skv-headless/react-native-scrollable-tab-view/blob/master/DefaultTabBar.js#L41

see #311


'DataFrame' object has no attribute 'mean_market_returns'

First of all, thanks for sharing this code.
I'm trying to run the notebook keras-ddpg and I ran into this error:
During the agent.fit() method there is a callback to TrainEpisodeLoggerPortfolio which evaluates the mean_market_return based on the environment infos attribute:
df = pd.DataFrame(self.env.infos)
self.episode_metrics[episode]=dict(
  max_drawdown=MDD(df.portfolio_value),
  sharpe=sharpe(df.rate_of_return),
  accumulated_portfolio_value=df.portfolio_value.iloc[-1],
  mean_market_return=df.mean_market_returns.cumprod().iloc[-1],
  cash_bias=df.weights.apply(lambda x:x[0]).mean()
)

The problem here seems to be that the Environment doesn't have mean_market_returns. Same thing is happening for the cash_bias since self.env.infos doesn't have weights, therefore the error (If I am correct those two attributes should be in the class PortfolioSim).
Am I doing something wrong or this is really the problem here?
This is the complete stack trace:
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-20-982fd62f6724> in <module>()
      6                       TrainIntervalLoggerTQDMNotebook(),
      7                       TrainEpisodeLoggerPortfolio(10),
----> 8                       ModelIntervalCheckpoint(save_path, 10*1440, 1)
      9                     ]
     10                  )

/usr/local/lib/python3.4/dist-packages/rl/core.py in fit(self, env, nb_steps, action_repetition, callbacks, verbose, visualize, nb_max_start_steps, start_step_policy, log_interval, nb_max_episode_steps)
    160                         'nb_steps': self.step,
    161                     }
--> 162                     callbacks.on_episode_end(episode, episode_logs)
    163
    164                     episode += 1

/usr/local/lib/python3.4/dist-packages/rl/callbacks.py in on_episode_end(self, episode, logs)
     55             # If not, fall back to `on_epoch_end` to be compatible with built-in Keras callbacks.
     56             if callable(getattr(callback, 'on_episode_end', None)):
---> 57                 callback.on_episode_end(episode, logs=logs)
     58             else:
     59                 callback.on_epoch_end(episode, logs=logs)

<ipython-input-19-9b518044e729> in on_episode_end(self, episode, logs)
     16             accumulated_portfolio_value=df.portfolio_value.iloc[-1],
     17             #mean_market_return=df.mean_market_returns.cumprod().iloc[-1],
---> 18             cash_bias=df.weights.apply(lambda x:x[0]).mean()
     19         )
     20

/usr/local/lib/python3.4/dist-packages/pandas/core/generic.py in __getattr__(self, name)
   3079             if name in self._info_axis:
   3080                 return self[name]
-> 3081             return object.__getattribute__(self, name)
   3082
   3083     def __setattr__(self, name, value):

AttributeError: 'DataFrame' object has no attribute 'weights'

1440/|/reward=-0.0000 info=(return: 0.9938, portfolio_value: 0.7632, cost: 0.0000, weights_std: 0.3301, reward: -0.0000, weights_mean: 0.1667, steps: 1441.0000, market_value: 1.2144, rate_of_return: -0.0026, date:<PHONE_NUMBER>.0000, log_return: -0.0026, )  0%|| 1440/2000000.0 [03:30<83:43:20,  6.63it/s]

Thanks again, you've done a great job!!

Sorry about that. I'm afraid the keras-ddpg notebook it outdated, I should remove it. That's because keras-rl isn't maintained anymore. You can either go back to an earlier commit or try the tensorforce notebook.

@wassname thanks for the reply.
I will try the notebook you mentioned.
kudos to you.


Cannot create alias inside record inline

Constructing a type alias inside a record gives an "Undefined variable" error.
Example
// This doesn't work
{ MyInt = Int }

// But this does
type MyInt = Int
{ MyInt }

Error message
error: Undefined variable `Int`

What happens here is that the right hand side gets treated as an expression since whether an identifier is a type/constructor or a regular identifier isn't communicated to the parser. This can be solved by splitting the identifier token into two the fixing the fallout in the parser.
However I am coming around to thinking the uppercase constructor/type and lower case variable scheme is a poor idea in the first place since it does not translate to operators and it would be nice to be able to define the list cons constructor as :: so pattern matching could be | x :: xs instad of | Cons x xs for instance.
To disambiguate type fields from value fields in record expression one would then need to write  { type MyInt = Int } instead. { MyInt } could still be allowed as a type field since it wouldn't be ambiguous that ``MyInt` refers to a type in that case.


MuiImageList

Handling the Imagelist

@manikandanmohan10 Please review the code and commit in the main branch

@Antony-M1 Please approve the pull request

@Antony-M1 Thanks for locking the conversation


ReadableArray cannot be converted to WritableArray

I'm encountering the following error in java
error: incompatible types: ReadableArray cannot be converted to WritableArray
          WritableArray phoneNumbers = contact.getArray("phoneNumbers");

the offending code is
https://github.com/rt2zz/react-native-contacts/blob/optimizeAndroidGetAll/android/src/main/java/com/rt2zz/reactnativecontacts/ContactsManager.java#L88
could anyone more familiar with java give me some tips on how to solve this?
The code is grabbing an existing contact and trying to insert a new phone/email into a json value that is an array.

Curcumvented the issue by changing the logic to build the WritableArray and pushing them only once into the resultset.


Add possibility to "mark as reviewed " without comment failed/aborted test runs

Description
Add possibility to "mark as reviewed " without comment failed/aborted test runs
Steps

Open test runt tab
Click on 3 dots on passed test run
Select "mark as reviewed"
Click "mark as reviewed"

Actual result: User is able to mark as reviewed without comment only passed test runs.
Expected result: User is able to mark as reviewed without comment any test run

fixed on UI from v. <IP_ADDRESS>4-SNAPSHOT

Verified in ui: <IP_ADDRESS>0-SNAPSHOT server: <IP_ADDRESS>7-SNAPSHOT.


issue with loading on boot with init.d

Ive got Homebridge working nicely. Login with SSH and type the command 'homebridge' and it starts with all the stuff I want. Everything works.
The only thing not working is to start at boot. Ive got the feeling that the start script is already running but my DHCP server have not given a ip adres. But Im not a technical guy, im the UX'er ;)
Below is the homebridge.log and the init.d/homebridge script
Love to hear what is going wrong
Content from homebridge.log:
[11/22/2016, 12:58:55 PM] Loaded plugin: homebridge-evohome
[11/22/2016, 12:59:03 PM] Registering platform 'homebridge-evohome.Evohome'
[11/22/2016, 12:59:03 PM] ---
[11/22/2016, 12:59:04 PM] Loaded plugin: homebridge-ifttt
[11/22/2016, 12:59:04 PM] Registering platform 'homebridge-ifttt.IFTTT'
[11/22/2016, 12:59:04 PM] ---
[11/22/2016, 12:59:05 PM] Loaded plugin: homebridge-nest
[11/22/2016, 12:59:06 PM] Registering platform 'homebridge-nest.Nest'
[11/22/2016, 12:59:06 PM] ---
[11/22/2016, 12:59:07 PM] Loaded plugin: homebridge-netatmo
[11/22/2016, 12:59:07 PM] Registering platform 'homebridge-netatmo.netatmo'
[11/22/2016, 12:59:07 PM] ---
[11/22/2016, 12:59:11 PM] Loaded plugin: homebridge-sonos
[11/22/2016, 12:59:11 PM] Registering accessory 'homebridge-sonos.Sonos'
[11/22/2016, 12:59:11 PM] ---
[11/22/2016, 12:59:11 PM] Loaded config.json with 1 accessories and 4 platforms.
[11/22/2016, 12:59:11 PM] ---
[11/22/2016, 12:59:11 PM] Loading 4 platforms...
[11/22/2016, 12:59:11 PM] [netatmo platform] Initializing netatmo platform...
[11/22/2016, 12:59:11 PM] [netatmo platform] Creating NetatmoPlatform...
[11/22/2016, 12:59:11 PM] Initializing Nest platform...
[11/22/2016, 12:59:11 PM] Fetching Nest devices.
[11/22/2016, 12:59:11 PM] [IFTTT] Initializing IFTTT platform...
[11/22/2016, 12:59:11 PM] [IFTTT] Loading accessories...
[11/22/2016, 12:59:11 PM] [IFTTT] Found: Accessory 1
[11/22/2016, 12:59:11 PM] [IFTTT] Loading service: A1-1, subtype: T1-1OnT1-1Off
[11/22/2016, 12:59:11 PM] [IFTTT] Loading service: A1-2, subtype: T1-2OnT1-2Off
[11/22/2016, 12:59:11 PM] [IFTTT] Loading service: A1-3, subtype: T1-3
[11/22/2016, 12:59:11 PM] [IFTTT] Loading service: A1-4, subtype: T1-4
[11/22/2016, 12:59:11 PM] [IFTTT] Initializing platform accessory 'Accessory 1'...
[11/22/2016, 12:59:11 PM] [Evohome] Initializing Evohome platform...
[11/22/2016, 12:59:11 PM] [Evohome] Logging into Evohome...
[11/22/2016, 12:59:11 PM] Loading 1 accessories...
[11/22/2016, 12:59:11 PM] [Woonkamer Speakers] Initializing Sonos accessory...
[11/22/2016, 12:59:32 PM] [Woonkamer Speakers] Found a playable coordinator device at <IP_ADDRESS> in zone 'Huiskamer' for accessory 'Woonkamer Speakers' in accessory room 'Huiskamer'
[11/22/2016, 12:59:55 PM] Software version for Upstairs Nest Protect is: 3.1rc9
[11/22/2016, 12:59:55 PM] Software version for Downstairs Nest Protect is: 3.1rc9
[11/22/2016, 12:59:55 PM] Initializing platform accessory 'Upstairs Nest Protect'...
[11/22/2016, 12:59:55 PM] Initializing platform accessory 'Downstairs Nest Protect'...
[11/22/2016, 1:00:03 PM] [Evohome] Error during Login: { Error: getaddrinfo ENOTFOUND tccna.honeywell.com tccna.honeywell.com:443
at errnoException (dns.js:28:10)
at GetAddrInfoReqWrap.onlookup [as oncomplete] (dns.js:76:26)
code: 'ENOTFOUND',
errno: 'ENOTFOUND',
syscall: 'getaddrinfo',
hostname: 'tccna.honeywell.com',
host: 'tccna.honeywell.com',
port: 443 }
[11/22/2016, 1:00:03 PM] [netatmo platform] ERROR - Netatmo: Error: Authenticate error: No response
Code from init.d/homebridge
#!/bin/sh
BEGIN INIT INFO
Provides: homebridge
Required-Start: $network $remote_fs $syslog
Required-Stop: $remote_fs $syslog
Default-Start: 2 3 4 5
Default-Stop: 0 1 6
Short-Description: Start daemon at boot time
Description: Enable service provided by daemon.
END INIT INFO
dir="/home/pi"
cmd="DEBUG=* /usr/bin/homebridge"
user="pi"
name=basename $0
pid_file="/var/run/$name.pid"
stdout_log="/var/log/$name.log"
stderr_log="/var/log/$name.err"
get_pid() {
cat "$pid_file"
}
is_running() {
[ -f "$pid_file" ] && ps get_pid > /dev/null 2>&1
}
case "$1" in
start)
if is_running; then
echo "Already started"
else
echo "Starting $name"
cd "$dir"
if [ -z "$user" ]; then
sudo $cmd >> "$stdout_log" 2>> "$stderr_log" &
else
sudo -u "$user" $cmd >> "$stdout_log" 2>> "$stderr_log" &
fi
echo $! > "$pid_file"
if ! is_running; then
echo "Unable to start, see $stdout_log and $stderr_log"
exit 1
fi
fi
;;
stop)
if is_running; then
echo -n "Stopping $name.."
kill get_pid
for i in {1..10}
do
if ! is_running; then
break
fi
        echo -n "."
        sleep 1
    done
    echo

    if is_running; then
        echo "Not stopped; may still be shutting down or shutdown may have failed"
        exit 1
    else
        echo "Stopped"
        if [ -f "$pid_file" ]; then
            rm "$pid_file"
        fi
    fi
else
    echo "Not running"
fi
;;
restart)
$0 stop
if is_running; then
    echo "Unable to stop, will not attempt to start"
    exit 1
fi
$0 start
;;
status)
if is_running; then
    echo "Running"
else
    echo "Stopped"
    exit 1
fi
;;
*)
echo "Usage: $0 {start|stop|restart|status}"
exit 1
;;

esac
exit 0

Do you have systemd on your Pi? If so, consider installing homebridge as a systemd service, as explained here. It has a benefit of being much easier to understand than horrendous init.d scripts. (And it waits for the network to be up).
Alternatively, you may set up homebridge as an ifup.d script, which will also ensure, that it's started after the network is fully up, see the first answer here.

changed the setting of my Raspberry Pi3 from a dynamic IP (DHCP) to a static IP and the problem was fixed.


SDK changes to support new version of swagger Resources API 2020-06-01

SDK changes to support new version of swagger Resources API 2020-06-01
There's some work being done on the service side which has to go in before this is merged, but I'd like to start the review off on this.

LGTM. Waiting for service status to be updated.

public class LiveDeploymentTests : TestBase

Do you mind adding a test for the statusMessage update we made?

Refers to: sdk/resources/Microsoft.Azure.Management.Resource/tests/ScenarioTests/DeploymentTests.ScenarioTests.cs:18 in fd9e77b. [](commit_id = fd9e77b018afe564b18914c6b655957004a15c7e, deletion_comment = True)

public class LiveDeploymentTests : TestBase

Do you mind adding a test for the statusMessage update we made?
Refers to: sdk/resources/Microsoft.Azure.Management.Resource/tests/ScenarioTests/DeploymentTests.ScenarioTests.cs:18 in fd9e77b. [](commit_id = fd9e77b, deletion_comment = True)

I added a test for this in InMemoryTests. I was waiting for statusMessage update to be fixed completely before adding a test in LiveDeploymentTests.

LGTM

Anything else to add to this PR?
PS there are merging conflicts

Anything else to add to this PR?
PS there are merging conflicts

I think we have everything we need. We should be okay to merge this now. I'll push a commit fixing merge issues in a while.

All changes are in.

@isra-fel mind helping merge the PR? We have another minor SDK update for resources that is pending on this.


Shallow multiloses

Thank you for sharing your solution. To keep the baseline repository consistent throughout the challenge, now solutions will not be merged. If you have any questions, do not hesitate to ask.


te.getVersionInfo() fails on latest release

If i type te.getVersionInfo() I get:
te.getVersionInfo()
Traceback (most recent call last):
File "", line 1, in
te.getVersionInfo()
File "C:\Tellurium-Winpython-3.7\python-3.7.7.amd64\lib\site-packages\tellurium\tellurium.py", line 212, in getVersionInfo
('antimony', antimony.version),
AttributeError: module 'antimony' has no attribute 'version'

I found that this issue is present on linux as well. I've rebuilt and reuploaded antimony for linux. The fix was to add a module-level attribute __version__ in __init__.py.
For future antimony builds, I suggest having __init__.py automatically fetch the version string using the code provided in this SO post.
However te.getVersionInfo() still doesn't work right now since the tesedml wheels were built incorrectly. I'll rebuild those now.

ok thanks!
H
On Thu, Aug 6, 2020 at 2:00 PM Gary Geng<EMAIL_ADDRESS>wrote:

I found that this issue is present on linux as well. I've rebuilt and
reuploaded antimony for linux. The fix was to add a module-level attribute
version in init.py.
For future antimony builds, I suggest having init.py automatically
fetch the version string using the code provided in this
https://stackoverflow.com/a/17638236/9171534 SO post.
However te.getVersionInfo() still doesn't work right now since the
tesedml wheels were built incorrectly. I'll rebuild those now.
—
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Reply to this email directly, view it on GitHub
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--
Herbert Sauro, Professor
University of Washington, Bioengineering
206-685-2119, www.sys-bio.org
<EMAIL_ADDRESS>Books: http://books.analogmachine.org/

PS If you want to update the way we handle version go ahead. I think I
used what you suggested in a recent package I helped write.
H
On Thu, Aug 6, 2020 at 2:39 PM Herbert M Sauro<EMAIL_ADDRESS>wrote:

ok thanks!
H
On Thu, Aug 6, 2020 at 2:00 PM Gary Geng<EMAIL_ADDRESS>wrote:

I found that this issue is present on linux as well. I've rebuilt and
reuploaded antimony for linux. The fix was to add a module-level attribute
version in init.py.
For future antimony builds, I suggest having init.py automatically
fetch the version string using the code provided in this
https://stackoverflow.com/a/17638236/9171534 SO post.
However te.getVersionInfo() still doesn't work right now since the
tesedml wheels were built incorrectly. I'll rebuild those now.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/sys-bio/tellurium/issues/465#issuecomment-670188525,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAIBSDRDYHPJUFG4SITZUNLR7MKQDANCNFSM4PW4DINQ
.

--
Herbert Sauro, Professor
University of Washington, Bioengineering
206-685-2119, www.sys-bio.org
<EMAIL_ADDRESS>Books: http://books.analogmachine.org/

--
Herbert Sauro, Professor
University of Washington, Bioengineering
206-685-2119, www.sys-bio.org
<EMAIL_ADDRESS>Books: http://books.analogmachine.org/

Sure, I'll do that. Also I think phrasedml is suffering from the same issue.
However, I don't think I have access to the sourceforge svn repo. Lucian, can you give me access? Or I can detail the changes I made and you can push it.

I'll need a new linux pip installer once you're ready.
Herbert
On Thu, Aug 6, 2020 at 3:42 PM Gary Geng<EMAIL_ADDRESS>wrote:

Sure, I'll do that. Also I think phrasedml is suffering from the same
issue.
However, I don't think I have access to the sourceforge svn repo. Lucian,
can you give me access? Or I can detail the changes I made and you can push
it.
—
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Reply to this email directly, view it on GitHub
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--
Herbert Sauro, Professor
University of Washington, Bioengineering
206-685-2119, www.sys-bio.org
<EMAIL_ADDRESS>Books: http://books.analogmachine.org/

I'm more than happy to get you access to svn's phrasedml.  However, as I
discovered today, there are actually two versions out there, because at
some point, phrasedml was copied over to github/sys-bio, and further
updates were made there.  I was just working on the mac release of that,
and made some updates to let it compile there.
Also, that version has a fixed init.py file anyway, so let's move away
from the sf version.  If you don't have access to the github/phrasedml
version, let me know!
-Lucian
On Thu, Aug 6, 2020 at 3:43 PM Gary Geng<EMAIL_ADDRESS>wrote:

Sure, I'll do that. Also I think phrasedml is suffering from the same
issue.
However, I don't think I have access to the sourceforge svn repo. Lucian,
can you give me access? Or I can detail the changes I made and you can push
it.
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That'll work, thanks!
I also need to modify antimony; I've added only two lines to __init__.py, so I think it might be easier for me to send it to you?
Also, I don't think I've worked with a tellurium installer. Where should I go to build that after the fixes are made?

The good news here is that Tellurium itself doesn't need to be re-installed:  it's pure python, so it only needs to be build/uploaded in one place.  And the failing function was calling the library functions, so when those libraries are updated, the function will Just Work.
Herbert, I have now uploaded new Windows versions of everything that didn't have a version attribute.  You can get the new ones by entering (inside Spyder, even):
pip install --upgrade antimony tesbml tesedml tecombine tenuml

The linux versions should work now as well.

Ok great try the Linux version. I’ve got a browser web page to talk to
tellurium in a docker image. This is for work with Veronica.
Herbert
On Fri, Aug 7, 2020 at 6:56 PM Gary Geng<EMAIL_ADDRESS>wrote:

The linux versions should work now as well.
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--
Herbert Sauro, Professor
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<EMAIL_ADDRESS>Books: http://books.analogmachine.org/

Hi,
I am working with Tellurium package and the te.getVersionInfo() still doesn't work for the tesedml. I am using Windows and Python 3.7.1., and my installed Tellurium package is 2.1.6 and tesedml is <IP_ADDRESS>.
Is there a way for me to resolve the issue? Thank you so much.

Hi, JingWiu!  I have tested this on a running VM of ubuntu, and 'getVersionInfo' works there, which means that there must be something different in your Travis CI setup that is the source of the problem.
Can you send us (or copy into a comment) the contents of your .travis.yml file (or the relevant bits from it) so we can test ourselves?  Thank you!

Hi Lucian,
Please find attached the information when running Travis CI. The error
appeared as follows when we tried to use the exportInlineOmex function from
Tellurium.
def VersionDict():
'''Return dict of version strings.'''
import tesbml, tesedml, tecombine
return {
'tellurium': getTelluriumVersion(),
'roadrunner':
roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
'antimony': antimony.version,
'phrasedml': phrasedml.version,
'tesbml': libsbml.getLibSBMLDottedVersion(),

      'tesedml': tesedml.__version__,

        'tecombine': tecombine.__version__
        }

E       AttributeError: module 'tesedml' has no attribute 'version'
FYI, I managed to run without error on my own computer (Windows). Please
find attached the pip list for your reference.
On Wed, Oct 28, 2020 at 4:58 AM Lucian Smith<EMAIL_ADDRESS>wrote:

Hi, JingWiu! I have tested this on a running VM of ubuntu, and
'getVersionInfo' works there, which means that there must be something
different in your Travis CI setup that is the source of the problem.
Can you send us (or copy into a comment) the contents of your .travis.yml
file (or the relevant bits from it) so we can test ourselves? Thank you!
—
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https://github.com/sys-bio/tellurium/issues/465#issuecomment-717534935,
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Package                            Version             Location

alabaster                          0.7.12
anaconda-client                    1.7.2
anaconda-navigator                 1.9.12
anaconda-project                   0.8.3
antimony                           <IP_ADDRESS>
appdirs                            1.4.4
argh                               0.26.2
asn1crypto                         1.3.0
astroid                            2.4.2
astropy                            4.0.1.post1
atomicwrites                       1.4.0
attrs                              19.3.0
autopep8                           1.5.3
Babel                              2.8.0
backcall                           0.2.0
backports.functools-lru-cache      1.6.1
backports.shutil-get-terminal-size 1.0.0
backports.tempfile                 1.0
backports.weakref                  1.0.post1
bcrypt                             3.1.7
beautifulsoup4                     4.9.1
biopython                          1.78
bitarray                           1.4.0
bkcharts                           0.2
bleach                             3.1.5
bokeh                              2.1.1
boto                               2.49.0
Bottleneck                         1.3.2
brotlipy                           0.7.0
certifi                            2020.6.20
cffi                               1.14.0
chardet                            3.0.4
click                              7.1.2
cloudpickle                        1.5.0
clyent                             1.2.2
colorama                           0.4.3
comtypes                           1.1.7
conda                              4.8.3
conda-build                        3.18.11
conda-package-handling             1.7.0
conda-verify                       3.4.2
contextlib2                        0.6.0.post1
cryptography                       2.9.2
cycler                             0.10.0
Cython                             0.29.21
cytoolz                            0.10.1
dask                               2.20.0
decorator                          4.4.2
defusedxml                         0.6.0
diff-match-patch                   20200713
distributed                        2.20.0
dnaplotlib                         1.0
docutils                           0.16
entrypoints                        0.3
et-xmlfile                         1.0.1
fastcache                          1.1.0
filelock                           3.0.12
flake8                             3.8.3
Flask                              1.1.2
fsspec                             0.7.4
future                             0.18.2
fuzzywuzzy                         0.18.0
gevent                             20.6.2
glob2                              0.7
gmpy2                              2.0.8
greenlet                           0.4.16
h5py                               2.10.0
HeapDict                           1.0.1
html5lib                           1.1
idna                               2.10
imageio                            2.9.0
imagesize                          1.2.0
importlib-metadata                 1.7.0
intervaltree                       3.0.2
ipykernel                          5.3.2
ipython                            7.16.1
ipython-genutils                   0.2.0
ipywidgets                         7.5.1
isort                              4.3.21
itsdangerous                       1.1.0
jdcal                              1.4.1
jedi                               0.17.1
Jinja2                             2.11.2
joblib                             0.16.0
json5                              0.9.5
jsonschema                         3.2.0
jupyter                            1.0.0
jupyter-client                     6.1.6
jupyter-console                    6.1.0
jupyter-core                       4.6.3
jupyterlab                         2.1.5
jupyterlab-server                  1.2.0
keyring                            21.2.1
kiwisolver                         1.2.0
lazy-object-proxy                  1.4.3
libarchive-c                       2.9
libroadrunner                      2.0.0
llvmlite                           0.33.0+1.g022ab0f
locket                             0.2.0
lxml                               4.5.2
MarkupSafe                         1.1.1
matplotlib                         3.2.2
mccabe                             0.6.1
menuinst                           1.4.16
mistune                            0.8.4
mkl-fft                            1.1.0
mkl-random                         1.1.1
mkl-service                        2.3.0
mock                               4.0.2
more-itertools                     8.4.0
mpmath                             1.1.0
msgpack                            1.0.0
multipledispatch                   0.6.0
navigator-updater                  0.2.1
nbconvert                          5.6.1
nbformat                           5.0.7
networkx                           2.4
nltk                               3.5
nose                               1.3.7
notebook                           6.0.3
numba                              0.50.1
numexpr                            2.7.1
numpy                              1.19.2
numpydoc                           1.1.0
olefile                            0.46
openpyxl                           3.0.4
packaging                          20.4
pandas                             1.0.5
pandocfilters                      1.4.2
paramiko                           2.7.1
parso                              0.7.0
partd                              1.1.0
path                               13.1.0
pathlib2                           2.3.5
pathtools                          0.1.2
patsy                              0.5.1
pep8                               1.7.1
pexpect                            4.8.0
phrasedml                          1.0.10
pickleshare                        0.7.5
Pillow                             7.2.0
pip                                20.1.1
pkginfo                            <IP_ADDRESS>
plotly                             4.11.0
pluggy                             0.13.1
ply                                3.11
prometheus-client                  0.8.0
prompt-toolkit                     3.0.5
psutil                             5.7.0
py                                 1.9.0
pycodestyle                        2.6.0
pycosat                            0.6.3
pycparser                          2.20
pycurl                             <IP_ADDRESS>
pydocstyle                         5.0.2
pyflakes                           2.2.0
Pygments                           2.6.1
pylint                             2.5.3
PyNaCl                             1.4.0
pyodbc                             4.0.0-unsupported
pyOpenSSL                          19.1.0
pyparsing                          2.4.7
pyreadline                         2.1
pyrsistent                         0.16.0
PySocks                            1.7.1
pytest                             5.4.3
python-dateutil                    2.8.1
python-jsonrpc-server              0.3.4
python-language-server             0.34.1
pytz                               2020.1
PyWavelets                         1.1.1
pywin32                            227
pywin32-ctypes                     0.2.0
pywinpty                           0.5.7
PyYAML                             5.3.1
pyzmq                              19.0.1
QDarkStyle                         2.8.1
QtAwesome                          0.7.2
qtconsole                          4.7.5
QtPy                               1.9.0
regex                              2020.6.8
reportlab                          3.5.54
requests                           2.24.0
retrying                           1.3.3
rope                               0.17.0
Rtree                              0.9.4
ruamel-yaml                        0.15.87
SALib                              1.3.11
sbml2matlab                        1.2.3
scikit-image                       0.16.2
scikit-learn                       0.23.1
scipy                              1.5.3
seaborn                            0.10.1
Send2Trash                         1.5.0
setuptools                         49.2.0.post20200714
simplegeneric                      0.8.1
singledispatch                     <IP_ADDRESS>
sip                                4.19.13
six                                1.15.0
snowballstemmer                    2.0.0
sortedcollections                  1.2.1
sortedcontainers                   2.2.2
soupsieve                          2.0.1
Sphinx                             3.1.2
sphinxcontrib-applehelp            1.0.2
sphinxcontrib-devhelp              1.0.2
sphinxcontrib-htmlhelp             1.0.3
sphinxcontrib-jsmath               1.0.1
sphinxcontrib-qthelp               1.0.3
sphinxcontrib-serializinghtml      1.1.4
sphinxcontrib-websupport           1.2.3
spyder                             4.1.4
spyder-kernels                     1.9.2
SQLAlchemy                         1.3.18
statsmodels                        0.11.1
sympy                              1.6.1
synbiopython                       0.0.1               c:\users\jingwui\dropbox\post_doc_documents\git_synbiopython_revised2\synbiopython
tables                             3.6.1
tblib                              1.6.0
tecombine                          <IP_ADDRESS>
tellurium                          2.1.6
tenuml                             <IP_ADDRESS>
terminado                          0.8.3
tesbml                             <IP_ADDRESS>
tesedml                            <IP_ADDRESS>
testpath                           0.4.4
threadpoolctl                      2.1.0
toml                               0.10.1
toolz                              0.10.0
tornado                            6.0.4
tqdm                               4.47.0
traitlets                          4.3.3
typing-extensions                  <IP_ADDRESS>
ujson                              1.35
unicodecsv                         0.14.1
urllib3                            1.25.9
watchdog                           0.10.3
wcwidth                            0.2.5
webencodings                       0.5.1
Werkzeug                           1.0.1
wheel                              0.34.2
widgetsnbextension                 3.5.1
win-inet-pton                      1.1.0
win-unicode-console                0.5
wincertstore                       0.2
wrapt                              1.11.2
xlrd                               1.2.0
XlsxWriter                         1.2.9
xlwings                            0.19.5
xlwt                               1.3.0
xmltodict                          0.12.0
yapf                               0.30.0
zict                               2.0.0
zipp                               3.1.0
zope.event                         4.4
zope.interface                     4.7.1
Build system information
Build language: python
Build dist: xenial
Build id: 193487276
Job id: 410224012
Runtime kernel version: 4.15.0-1077-gcp
travis-build version: acd5a925
Build image provisioning date and time
Wed Jun 24 13:36:52 UTC 2020
Operating System Details
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.6 LTS
Release:	16.04
Codename:	xenial
Systemd Version
systemd 229
Cookbooks Version
3f92a99 https://github.com/travis-ci/travis-cookbooks/tree/3f92a99
git version
git version 2.27.0
bash version
GNU bash, version 4.3.48(1)-release (x86_64-pc-linux-gnu)
gcc version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
docker version
Client:
Version:           18.06.0-ce
API version:       1.38
Go version:        go1.10.3
Git commit:        0ffa825
Built:             Wed Jul 18 19:11:02 2018
OS/Arch:           linux/amd64
Experimental:      false
Server:
Engine:
Version:          18.06.0-ce
API version:      1.38 (minimum version 1.12)
Go version:       go1.10.3
Git commit:       0ffa825
Built:            Wed Jul 18 19:09:05 2018
OS/Arch:          linux/amd64
Experimental:     false
clang version
clang version 7.0.0 (tags/RELEASE_700/final)
jq version
jq-1.5
bats version
Bats 0.4.0
shellcheck version
0.7.0
shfmt version
v2.6.3
ccache version
3.2.4
cmake version
cmake version 3.12.4
heroku version
heroku/7.42.1 linux-x64 node-v12.16.2
imagemagick version
Version: ImageMagick 6.8.9-9 Q16 x86_64 2019-11-12 http://www.imagemagick.org
md5deep version
4.4
mercurial version
version 4.8
mysql version
mysql  Ver 14.14 Distrib 5.7.30, for Linux (x86_64) using  EditLine wrapper
openssl version
OpenSSL 1.0.2g  1 Mar 2016
packer version
1.3.3
postgresql client version
psql (PostgreSQL) 10.13 (Ubuntu 10.13-1.pgdg16.04+1)
ragel version
Ragel State Machine Compiler version 6.8 Feb 2013
sudo version
1.8.16
gzip version
gzip 1.6
zip version
Zip 3.0
vim version
VIM - Vi IMproved 7.4 (2013 Aug 10, compiled Mar 18 2020 14:06:17)
iptables version
iptables v1.6.0
curl version
curl 7.47.0 (x86_64-pc-linux-gnu) libcurl/7.47.0 GnuTLS/3.4.10 zlib/1.2.8 libidn/1.32 librtmp/2.3
wget version
GNU Wget 1.17.1 built on linux-gnu.
rsync version
rsync  version 3.1.1  protocol version 31
gimme version
v1.5.4
nvm version
0.35.3
perlbrew version
/home/travis/perl5/perlbrew/bin/perlbrew  - App::perlbrew/0.88
phpenv version
rbenv 1.1.2-30-gc879cb0
rvm version
rvm 1.29.10 (latest) by Michal Papis, Piotr Kuczynski, Wayne E. Seguin [https://rvm.io]
default ruby version
ruby 2.5.3p105 (2018-10-18 revision 65156) [x86_64-linux]
CouchDB version
couchdb 1.6.1
ElasticSearch version
5.5.0
Installed Firefox version
firefox 63.0.1
MongoDB version
MongoDB 4.0.19
PhantomJS version
2.1.1
Pre-installed PostgreSQL versions
9.4.26
9.5.22
9.6.18
Redis version
redis-server 6.0.5
Pre-installed Go versions
1.11.1
ant version
Apache Ant(TM) version 1.9.6 compiled on July 20 2018
mvn version
Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f)
gradle version
Gradle 5.1.1!
lein version
Leiningen 2.9.3 on Java 11.0.2 OpenJDK 64-Bit Server VM
Pre-installed Node.js versions
v10.21.0
v11.0.0
v12.18.1
v4.9.1
v6.17.1
v8.12.0
v8.17.0
v8.9
phpenv versions
system
5.6
5.6.40
7.1
7.1.27
7.2

7.2.15 (set by /home/travis/.phpenv/version)
hhvm
hhvm-stable
composer --version
Composer version 1.8.4 2019-02-11 10:52:10
Pre-installed Ruby versions
ruby-2.3.8
ruby-2.4.5
ruby-2.5.3
0.02s0.01s0.51s0.28s0.07s0.00s0.06s0.00s0.01s0.01s0.01s0.02s0.01s0.00s0.00s0.03s0.01s0.02s0.49s0.00s0.00s0.00s0.01s0.00s0.12s0.01s0.94s0.00s0.00s6.04s0.00s3.01s0.00s2.53s
docker_mtu
resolvconf
Downloading archive: https://storage.googleapis.com/travis-ci-language-archives/python/binaries/ubuntu/16.04/x86_64/python-3.8.3.tar.bz2
0.47s$ curl -sSf --retry 5 -o python-3.8.3.tar.bz2 ${archive_url}
11.83s$ sudo tar xjf python-3.8.3.tar.bz2 --directory /

$ source ~/virtualenv/python3.8.3/bin/activate
$ python --version
Python 3.8.3
$ pip --version
pip 20.1 from /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages/pip (python 3.8)
$ pip install --upgrade pip
Collecting pip
Downloading pip-20.2.4-py2.py3-none-any.whl (1.5 MB)
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 20.1
Uninstalling pip-20.1:
Successfully uninstalled pip-20.1
Successfully installed pip-20.2.4
$ pip install --upgrade coveralls pytest-cov pytest
Collecting coveralls
Downloading coveralls-2.1.2-py2.py3-none-any.whl (13 kB)
Collecting pytest-cov
Downloading pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB)
Collecting pytest
Downloading pytest-6.1.1-py3-none-any.whl (272 kB)
Collecting requests>=1.0.0
Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB)
Collecting coverage<6.0,>=4.1
Downloading coverage-5.3-cp38-cp38-manylinux1_x86_64.whl (230 kB)
Collecting docopt>=0.6.1
Downloading docopt-0.6.2.tar.gz (25 kB)
Collecting py>=1.8.2
Downloading py-1.9.0-py2.py3-none-any.whl (99 kB)
Requirement already satisfied, skipping upgrade: pluggy<1.0,>=0.12 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest) (0.13.1)
Collecting toml
Downloading toml-0.10.1-py2.py3-none-any.whl (19 kB)
Collecting iniconfig
Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Requirement already satisfied, skipping upgrade: attrs>=17.4.0 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest) (19.3.0)
Requirement already satisfied, skipping upgrade: packaging in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest) (20.3)
Collecting idna<3,>=2.5
Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB)
Collecting chardet<4,>=3.0.2
Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from requests>=1.0.0->coveralls) (2<IP_ADDRESS>)
Requirement already satisfied, skipping upgrade: six in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from packaging->pytest) (1.14.0)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from packaging->pytest) (2.4.7)
Building wheels for collected packages: docopt
Building wheel for docopt (setup.py) ... done
Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13704 sha256=d43c504f561bf73b0c6fd6c3d85b1d22666d562bb2bbf821e0c79016b18e07e7
Stored in directory: /home/travis/.cache/pip/wheels/56/ea/58/ead137b087d9e326852a851351d1debf4ada529b6ac0ec4e8c
Successfully built docopt
Installing collected packages: idna, urllib3, chardet, requests, coverage, docopt, coveralls, py, toml, iniconfig, pytest, pytest-cov
Attempting uninstall: py
Found existing installation: py 1.8.1
Uninstalling py-1.8.1:
Successfully uninstalled py-1.8.1
Attempting uninstall: pytest
Found existing installation: pytest 5.4.2
Uninstalling pytest-5.4.2:
Successfully uninstalled pytest-5.4.2
Successfully installed chardet-3.0.4 coverage-5.3 coveralls-2.1.2 docopt-0.6.2 idna-2.10 iniconfig-1.1.1 py-1.9.0 pytest-6.1.1 pytest-cov-2.10.1 requests-2.24.0 toml-0.10.1 urllib3-1.25.11
$ pip install -e .
Collecting pandas>=0.22
Downloading pandas-1.1.3-cp38-cp38-manylinux1_x86_64.whl (9.3 MB)
Collecting fuzzywuzzy
Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB)
Collecting dnaplotlib
Downloading dnaplotlib-1.0.tar.gz (17 kB)
Collecting tellurium
Downloading tellurium-2.1.6-py3-none-any.whl (117 kB)
Collecting tesbml
Downloading tesbml-<IP_ADDRESS>-cp38-cp38-manylinux2014_x86_64.whl (6.3 MB)
Collecting biopython
Downloading biopython-1.78-cp38-cp38-manylinux1_x86_64.whl (2.3 MB)
Collecting reportlab
Downloading reportlab-3.5.54-cp38-cp38-manylinux2010_x86_64.whl (2.6 MB)
Collecting nbgitpuller
Downloading nbgitpuller-0.9.0-py2.py3-none-any.whl (14 kB)
Requirement already satisfied: numpy>=1.15.4 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pandas>=0.22->synbiopython==0.0.1) (1.18.4)
Collecting pytz>=2017.2
Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting python-dateutil>=2.7.3
Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting scipy>=1.5.1
Downloading scipy-1.5.3-cp38-cp38-manylinux1_x86_64.whl (25.8 MB)
Requirement already satisfied: requests in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from tellurium->synbiopython==0.0.1) (2.24.0)
Collecting ipykernel>=4.6.1
Downloading ipykernel-5.3.4-py3-none-any.whl (120 kB)
Collecting ipython
Downloading ipython-7.18.1-py3-none-any.whl (786 kB)
Requirement already satisfied: appdirs>=1.4.3 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from tellurium->synbiopython==0.0.1) (1.4.4)
Collecting tenuml>=1.0.0
Downloading tenuml-<IP_ADDRESS>-cp38-cp38-manylinux2014_x86_64.whl (5.0 MB)
Collecting jupyter-core>=4.3.0
Downloading jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB)
Collecting libroadrunner>=2.0.0
Downloading libroadrunner-2.0.0-cp38-cp38-manylinux2014_x86_64.whl (54.3 MB)
Requirement already satisfied: pytest in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from tellurium->synbiopython==0.0.1) (6.1.1)
Collecting antimony>=2.12.0
Downloading antimony-<IP_ADDRESS>-py3-none-manylinux2010_x86_64.whl (5.8 MB)
Collecting jinja2>=2.9.6
Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting tesedml>=0.4.3
Downloading tesedml-<IP_ADDRESS>-cp38-cp38-manylinux2010_x86_64.whl (5.8 MB)
Collecting phrasedml>=1.0.9
Downloading phrasedml-<IP_ADDRESS>-cp38-cp38-manylinux2010_x86_64.whl (5.3 MB)
Collecting matplotlib>=2.0.2
Downloading matplotlib-3.3.2-cp38-cp38-manylinux1_x86_64.whl (11.6 MB)
Collecting tecombine>=0.2.2
Downloading tecombine-<IP_ADDRESS>-cp38-cp38-manylinux2010_x86_64.whl (5.2 MB)
Collecting plotly>=2.0.12
Downloading plotly-4.12.0-py2.py3-none-any.whl (13.1 MB)
Collecting sbml2matlab>=0.9.1
Downloading sbml2matlab-<IP_ADDRESS>-cp38-cp38-manylinux2014_x86_64.whl (10.9 MB)
Collecting jupyter-client>=5.1.0
Downloading jupyter_client-6.1.7-py3-none-any.whl (108 kB)
Collecting pillow>=4.0.0
Downloading Pillow-8.0.1-cp38-cp38-manylinux1_x86_64.whl (2.2 MB)
Collecting tornado
Downloading tornado-6.0.4.tar.gz (496 kB)
Collecting notebook>=5.5.0
Downloading notebook-6.1.4-py3-none-any.whl (9.5 MB)
Requirement already satisfied: six>=1.5 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from python-dateutil>=2.7.3->pandas>=0.22->synbiopython==0.0.1) (1.14.0)
Requirement already satisfied: idna<3,>=2.5 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from requests->tellurium->synbiopython==0.0.1) (2.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from requests->tellurium->synbiopython==0.0.1) (2<IP_ADDRESS>)
Requirement already satisfied: chardet<4,>=3.0.2 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from requests->tellurium->synbiopython==0.0.1) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from requests->tellurium->synbiopython==0.0.1) (1.25.11)
Collecting traitlets>=4.1.0
Downloading traitlets-5.0.5-py3-none-any.whl (100 kB)
Collecting pexpect>4.3; sys_platform != "win32"
Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Collecting decorator
Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting pygments
Downloading Pygments-2.7.2-py3-none-any.whl (948 kB)
Requirement already satisfied: setuptools>=18.5 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from ipython->tellurium->synbiopython==0.0.1) (46.1.3)
Collecting backcall
Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
Downloading prompt_toolkit-3.0.8-py3-none-any.whl (355 kB)
Collecting jedi>=0.10
Downloading jedi-0.17.2-py2.py3-none-any.whl (1.4 MB)
Collecting pickleshare
Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Requirement already satisfied: iniconfig in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest->tellurium->synbiopython==0.0.1) (1.1.1)
Requirement already satisfied: attrs>=17.4.0 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest->tellurium->synbiopython==0.0.1) (19.3.0)
Requirement already satisfied: py>=1.8.2 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest->tellurium->synbiopython==0.0.1) (1.9.0)
Requirement already satisfied: packaging in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest->tellurium->synbiopython==0.0.1) (20.3)
Requirement already satisfied: pluggy<1.0,>=0.12 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest->tellurium->synbiopython==0.0.1) (0.13.1)
Requirement already satisfied: toml in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest->tellurium->synbiopython==0.0.1) (0.10.1)
Collecting MarkupSafe>=0.23
Downloading MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl (32 kB)
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.2.0-cp38-cp38-manylinux1_x86_64.whl (92 kB)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from matplotlib>=2.0.2->tellurium->synbiopython==0.0.1) (2.4.7)
Collecting cycler>=0.10
Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting retrying>=1.3.3
Downloading retrying-1.3.3.tar.gz (10 kB)
Collecting pyzmq>=13
Downloading pyzmq-19.0.2-cp38-cp38-manylinux1_x86_64.whl (1.1 MB)
Collecting prometheus-client
Downloading prometheus_client-0.8.0-py2.py3-none-any.whl (53 kB)
Collecting argon2-cffi
Downloading argon2_cffi-20.1.0-cp35-abi3-manylinux1_x86_64.whl (97 kB)
Collecting nbconvert
Downloading nbconvert-6.0.7-py3-none-any.whl (552 kB)
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Downloading nbformat-5.0.8-py3-none-any.whl (172 kB)
Collecting Send2Trash
Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB)
Collecting terminado>=0.8.3
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Collecting ipython-genutils
Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting ptyprocess>=0.5
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Requirement already satisfied: wcwidth in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->tellurium->synbiopython==0.0.1) (0.1.9)
Collecting parso<0.8.0,>=0.7.0
Downloading parso-0.7.1-py2.py3-none-any.whl (109 kB)
Collecting cffi>=1.0.0
Downloading cffi-1.14.3-cp38-cp38-manylinux1_x86_64.whl (410 kB)
Collecting pandocfilters>=1.4.1
Downloading pandocfilters-1.4.3.tar.gz (16 kB)
Collecting jupyterlab-pygments
Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)
Collecting bleach
Downloading bleach-3.2.1-py2.py3-none-any.whl (145 kB)
Collecting mistune<2,>=0.8.1
Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting testpath
Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB)
Collecting defusedxml
Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Collecting nbclient<0.6.0,>=0.5.0
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Collecting entrypoints>=0.2.2
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Collecting jsonschema!=2.5.0,>=2.4
Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting pycparser
Downloading pycparser-2.20-py2.py3-none-any.whl (112 kB)
Collecting webencodings
Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting nest-asyncio
Downloading nest_asyncio-1.4.2-py3-none-any.whl (5.3 kB)
Collecting async-generator
Downloading async_generator-1.10-py3-none-any.whl (18 kB)
Collecting pyrsistent>=0.14.0
Downloading pyrsistent-0.17.3.tar.gz (106 kB)
Building wheels for collected packages: dnaplotlib, tornado, retrying, pandocfilters, pyrsistent
Building wheel for dnaplotlib (setup.py) ... done
Created wheel for dnaplotlib: filename=dnaplotlib-1.0-py3-none-any.whl size=20649 sha256=d2b4ce180b9dc596e24b7bde2581c2fd21b08d780319a493d9257b789da47ef2
Stored in directory: /home/travis/.cache/pip/wheels/8f/ce/3d/1e72484b51e74993b8933b3c145ef81cfd70a56d30d1228267
Building wheel for tornado (setup.py) ... done
Created wheel for tornado: filename=tornado-6.0.4-cp38-cp38-linux_x86_64.whl size=423023 sha256=ce878e60d5afc6b98a77571a41b738d0da37830cb12a84d0171f4d628f5711b5
Stored in directory: /home/travis/.cache/pip/wheels/88/79/e5/598ba17e85eccf2626eab62e4ee8452895636cd542650d450d
Building wheel for retrying (setup.py) ... done
Created wheel for retrying: filename=retrying-1.3.3-py3-none-any.whl size=11430 sha256=eebbcfaebbeed5c947ea26e198898ef08c31c85f390b416df25071d0b7f985fd
Stored in directory: /home/travis/.cache/pip/wheels/c4/a7/48/0a434133f6d56e878ca511c0e6c38326907c0792f67b476e56
Building wheel for pandocfilters (setup.py) ... done
Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7991 sha256=75e170d0e11461e605f5e5d5ff3beb05947e8e15cb9de487ae994b0822c8ffe0
Stored in directory: /home/travis/.cache/pip/wheels/fc/39/52/8d6f3cec1cca4ceb44d658427c35711b19d89dbc4914af657f
Building wheel for pyrsistent (setup.py) ... done
Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp38-cp38-linux_x86_64.whl size=114308 sha256=9316d510bd917f1b5629b7656f5c8528defab2865d8c510dd4cec86aa31476ec
Stored in directory: /home/travis/.cache/pip/wheels/3d/22/08/7042eb6309c650c7b53615d5df5cc61f1ea9680e7edd3a08d2
Successfully built dnaplotlib tornado retrying pandocfilters pyrsistent
Installing collected packages: pytz, python-dateutil, pandas, fuzzywuzzy, dnaplotlib, scipy, pyzmq, tornado, ipython-genutils, traitlets, jupyter-core, jupyter-client, ptyprocess, pexpect, decorator, pygments, backcall, prompt-toolkit, parso, jedi, pickleshare, ipython, ipykernel, tenuml, libroadrunner, tesbml, antimony, MarkupSafe, jinja2, tesedml, phrasedml, pillow, kiwisolver, cycler, matplotlib, tecombine, retrying, plotly, sbml2matlab, tellurium, biopython, reportlab, prometheus-client, pycparser, cffi, argon2-cffi, pandocfilters, pyrsistent, jsonschema, nbformat, jupyterlab-pygments, webencodings, bleach, mistune, testpath, defusedxml, nest-asyncio, async-generator, nbclient, entrypoints, nbconvert, Send2Trash, terminado, notebook, nbgitpuller, synbiopython
Running setup.py develop for synbiopython
ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.
We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.
libroadrunner 2.0.0 requires numpy>=1.19, but you'll have numpy 1.18.4 which is incompatible.
matplotlib 3.3.2 requires certifi>=2020.06.20, but you'll have certifi 2<IP_ADDRESS> which is incompatible.
tellurium 2.1.6 requires numpy>=1.19.0, but you'll have numpy 1.18.4 which is incompatible.
Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 antimony-<IP_ADDRESS> argon2-cffi-20.1.0
async-generator-1.10 backcall-0.2.0 biopython-1.78 bleach-3.2.1 cffi-1.14.3 cycler-0.10.0 decorator-4.4.2
defusedxml-0.6.0 dnaplotlib-1.0 entrypoints-0.3 fuzzywuzzy-0.18.0 ipykernel-5.3.4 ipython-7.18.1
ipython-genutils-0.2.0 jedi-0.17.2 jinja2-2.11.2 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.6.3
jupyterlab-pygments-0.1.2 kiwisolver-1.2.0 libroadrunner-2.0.0 matplotlib-3.3.2 mistune-0.8.4
nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nbgitpuller-0.9.0 nest-asyncio-1.4.2 notebook-6.1.4
pandas-1.1.3 pandocfilters-1.4.3 parso-0.7.1 pexpect-4.8.0 phrasedml-<IP_ADDRESS> pickleshare-0.7.5
pillow-8.0.1 plotly-4.12.0 prometheus-client-0.8.0 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pycparser-2.20
pygments-2.7.2 pyrsistent-0.17.3 python-dateutil-2.8.1 pytz-2020.1 pyzmq-19.0.2 reportlab-3.5.54
retrying-1.3.3 sbml2matlab-<IP_ADDRESS> scipy-1.5.3 synbiopython tecombine-<IP_ADDRESS> tellurium-2.1.6
tenuml-<IP_ADDRESS> terminado-0.9.1 tesbml-<IP_ADDRESS> tesedml-<IP_ADDRESS> testpath-0.4.4 tornado-6.0.4
traitlets-5.0.5 webencodings-0.5.1
../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/tellurium.py:695: in exportInlineOmex
saveInlineOMEX(inline_omex, export_location)
../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/teconverters/inline_omex.py:27: in saveInlineOMEX
omex = inlineOmex.fromString(omex_str)
../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/teconverters/inline_omex.py:199: in fromString
return inlineOmex(sources)
../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/teconverters/inline_omex.py:52: in init
description=DumpJSONInfo(),
../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/tellurium.py:1077: in DumpJSONInfo
'version_info': VersionDict()})

def VersionDict():
    '''Return dict of version strings.'''
    import tesbml, tesedml, tecombine
    return {
        'tellurium': getTelluriumVersion(),
        'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
        'antimony': antimony.__version__,
        'phrasedml': phrasedml.__version__,
        'tesbml': libsbml.getLibSBMLDottedVersion(),

      'tesedml': tesedml.__version__,

        'tecombine': tecombine.__version__
        }

E       AttributeError: module 'tesedml' has no attribute 'version'

Hi @luciansmith , thank you for looking into this and for developing this package. We intend to use it in synbiopython and here are the contents of the
travis.yml:
language: python
python:
  - "3.8.3"

# command to install dependencies
before_install:
  - pip --version
  - pip install --upgrade pip
  - pip --version
  - pip install --upgrade pytest pytest-cov coveralls
install:
  - pip install -e .
# command to run tests
script:
  - python -m pytest -v --cov synbiopython --cov-report term-missing

after_success:
  - coveralls

This build passed on travis on June 1, but not now, which means tesedml or tellurium had a new release which breaks the build: https://pypi.org/project/tesedml/#history
I hope these help.
Thanks

Hi @luciansmith,
With the provided details, do you have an idea of how we can resolve the issue? Let us know if any more information required.
Your advice on this matter would be greatly appreciated. Thank you.

OK!  I think I figured out the problem.
Somewhere in your own code, you define a function called "VersionDict".  From your description earlier I thought you were getting errors from tellurium's 'getVersionInfo()', but I don't think you are:
    def VersionDict():
        '''Return dict of version strings.'''
        import tesbml, tesedml, tecombine
        return {
            'tellurium': getTelluriumVersion(),
            'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
            'antimony': antimony.__version__,
            'phrasedml': phrasedml.__version__,
            'tesbml': libsbml.getLibSBMLDottedVersion(),
           'tesedml': tesedml.__version__,
           'tecombine': tecombine.__version__
            }

The problem is that version was indeed not defined for tesedml:  instead, you need to call the same thing that was used in tesbml:  'getLibSEDMLDottedVersion()'.
You can check what we use to find the version information from tellurium's 'getVersionInfo()', at line 204 of https://github.com/sys-bio/tellurium/blob/develop/tellurium/tellurium.py :
def getVersionInfo():
    """ Returns version information for tellurium included packages.
    :returns: list of tuples (package, version)
    """
    versions = [
        ('tellurium', getTelluriumVersion()),
        ('roadrunner', roadrunner.__version__),
        ('antimony', antimony.__version__),
    ]
    if libsbml:
        versions.append(('libsbml', libsbml.getLibSBMLDottedVersion()))
    if libsedml:
        versions.append(('libsedml', libsedml.getLibSEDMLDottedVersion()))
    if phrasedml:
        versions.append(('phrasedml', phrasedml.__version__))
    if sbol:
        versions.append(('pySBOL', sbol.__version__))
    return versions

Thank you for your reply! Actually, VersionDict() is defined in tellurium.py, not our code:
https://github.com/sys-bio/tellurium/blob/bf853af081d33ce950ebccd2d32615203ea8fb01/tellurium/tellurium.py#L1066
Are you intending to retire VersionDict()?

Oh!  One of the disadvantages of coming to the code late in its life is that there are all sorts of surprises like this buried in different places ;-)
So, yes, I will fix VersionDict(), and in the meantime, feel free to use getVersionInfo() instead, or to edit the code yourself to become:
def VersionDict():
    '''Return dict of version strings.'''
    import tesbml, tesedml, tecombine
    return {
        'tellurium': getTelluriumVersion(),
        'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
        'antimony': antimony.__version__,
        'phrasedml': phrasedml.__version__,
        'tesbml': libsbml.getLibSBMLDottedVersion(),
        'tesedml': tesedml.getLibSEDMLDottedVersion(),
        'tecombine': tecombine.getLibCombineDottedVersion(),
        }

(As it turned out, the same problem existed with tecombine.)

It is working now! @luciansmith Thank you so much for fixing that!

Great Thanks @JingWui for bringing it to our attention.


To use curl for oauth proxy protected URL

Hello,
Can anyone please tell me what would be the endpoint to be accessed to get access token when using google as provider.
Thanks

Google's OAuth documentation has sample code for this
https://developers.google.com/identity/protocols/OAuth2


[Feature]Enhancement Add hive-writer runtime profiles, change output file names and add hive_sink_max_open_partitions .

Proposed changes
Issue Number: #31442

Add hive-writer runtime profiles.
Change output file names to ${query_id}${uuid}-${index}.${compression}.${format}. e.g. "d8735c6fa444a6d-acd392981e510c2b_34fbdcbb-b2e1-4f2c-b68c-a384238954a9-0.snappy.parquet". For the same partition writer, when the file size exceeds hive_sink_max_file_size, the currently written file will be closed and a new file will be generated, in which ${index} in the new file name will be incremented, while the rest will be the same .
Add hive_sink_max_open_partitions to control max open partitions in hive sink.

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

run buildall

run buildall


Fix vm tests

What this PR does / why we need it:
Rework the VM lifecycle tests. It fixes the naming in the tests to be consistent and differentiate
between VM and VMI. The gomega matchers are now decorated with additional descriptions
making the debugging failed tests easier. Finally the eventually loops are now less time demanding
and in few cases check for equivalent events.
Overall this PR makes vm-tests faster and more stable.
Which issue(s) this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when PR gets merged):
Fixes #
Special notes for your reviewer:
One of the patches fixing the overall CI.
Release note:

NONE

This change is

@vladikr @stu-gott can you please take a look at this one? I would like to merge as soon as possible so I can continue with writing the guide for fixing the rest. Thanks

@petrkotas that one does not need a release note.

for reference: https://jenkins.ovirt.org/job/kubevirt_kubevirt_standard-check-pr/1962/artifact/ci_build_summary.html

ci test please

@petrkotas I see pretty often
[Fail] VirtualMachine A valid VirtualMachine given [It] should remove VirtualMachineInstance once the VM is marked for deletion
/root/go/src/kubevirt.io/kubevirt/tests/vm_test.go:214

fail now. Can it be that the timeout changes cause this?

@rmohr investigating the issue.

@rmohr I fixed it. I made the test check for delete timestamp, but forgot the vmi could be already gone. Fixed.

@davidvossel good review!

@davidvossel thanks for clarifications. Fixing it. Thinking about this, I would like to see information explaining what the tests verifies directly in the test itself. The current description is not enough.
Will figure out how to fix that.

Closing this, as I can no longer see the failures


Pi 5 Drivers

I have one of the OneInchEyes from the initial batch, but have not had a potentially compatible device until the Pi 5.
For the StarlightEye it looks like a driver for the Pi 5 is in development.
https://github.com/will127534/StarlightEye/issues/2
Does a similar driver need to be made for the IMX294? Or should the current driver and instructions work fine?

Yeap, I'm still working on it.....
I've tested OneInchEye, StarlightEye and IMX294 board all shows some issues on RPI5, I'm still figuring out what is happening.

imx283-v4l2-driver
I've updated the IMX283 driver here.

I am experiencing a similar issue as SamM-Springbok described initially regarding compatibility with the Pi 5. Have you resolved the problems with the OneInchEye on the RPi 5, or are there still issues to be aware of? Additionally, is the updated IMX283 driver applicable to this situation?
After completing the steps in the readme from this link: https://github.com/will127534/imx283-v4l2-driver how can I verify that my camera system works on RPi 5?
I went through Quick-Start-Guide  https://github.com/will127534/OneInchEye/wiki/OneInchEye-Quick-Start-Guide but when tried to execute the last command: rpicam-still -r -o test.jpg -f -t 0 an ERROR pops up stating: "rpicam-aps currently only supports the Raspberry Pi platforms..."
Are there are any major differences between OneInchEye V1.4 and OneInchEye V1.3? I have both, but don't have a CM4 board to test them.
Have you any information about the power consumption of the OneInchEye camera? I'm also trying to connect the OneInchEye to the FPGA with a 4-lane connector, but have some problems. Could the power consumption of the camera be the case?

Hi @Isonoglu
Yes, I have resolve the issues, I've actually updated the drivers and guide last week, now it should work if you follow the setup guide (I've also verified it is working on my RPI5).
For the error, have you restart your RPI5? I also got that error if I did not reboot after recompiling rpicam-apps, but after a reboot the message will goes away.
There is no difference in terms of the Sensor between v1.3 and v1.4, so they should be the same.
For the power consumption, I don't have that handy but I will say it shouldn't be a huge issue (I've run it with a 50cm length FPC cable), if you have other board that is not RPI manufactured, can you check if the enable pin on the FPC has asserted?  There is a enable signal on the FPC that will power up/down the sensor. Enable pin is also one of the difference between V1.3 and V1.4, on V1.4 you can solder the enable pin jumper to ignore that enable pin or default to pulled-high.

@Isonoglu Can you try re-install the v4l2 driver? I noticed that during the libcamera compiling, some package installed will trigger update-initramfs which then will caused dkms driver to disappear.

Hello, I just want to inform you that I went through the procedure in the Start Guide again and tried a different camera port, which resulted in success. You just need to change this line: 'sudo nano /boot/config.txt', because the config file isn't on that path. But everything else is straightforward."

@Isonoglu Thanks for the confirmation!
Also note that you can add ,cam0  to the dtoverlay to move the port to Cam 0 (By default it is using Cam 1 because historical reasons: RPI default uses cam0 interface because that is the only one with 4-lane MIPI).
I'll update the guide as your suggestion and also some ports indicator!
Thanks a lot !

Updated the quick start guide


SVGR Options & TypeScript

@pd4d10 Thanks for creating the plugin. Works nicely and I like that I can use both the default export for the src/path of the svg and the named export for the React component.
I was wondering if you would accept a PR to enable the plugin users to pass SVGR options (e.g. { plugins: ['@svgr/plugin-svgo'] }).
Also, I think the plugin should provide the typings to support this change to svg file imports. A simple client.d.ts with the typings suggested in #3 which is then added by the users to the tsconfig.json like "types": ["vite/client", "vite-plugin-svgr/client"] would be a solution.

I was wondering if you would accept a PR to enable the plugin users to pass SVGR options (e.g. { plugins: ['@svgr/plugin-svgo'] }).

Sure. PR's welcome!

BTW, plugins like svgo are more suitable for use in production mode.
Perhaps we can make it built-in and decide when to use it by https://vitejs.dev/config/#conditional-config

It looks like there are two PRs open to add svgr options: #11 and #13.

Fixed in v0.6.0. Thanks for @IanVS 's work!


SWDEV-351540 - ASAN packaging for rocm-core

Package only ASAN libraries
Component based install
Suffix "asan" added to package name
Change-Id: Ic758eefef27742df3a4a4301fd3661714de4bb36

To sync gerrit rocm-core with github, pulled the missing changes from gerrit to github

Already available in master branch


Discuss HA strategies for pageservers - Active/Standby

https://neondb.slack.com/archives/C033RQ5SPDH/p1678007277320459

I want to raise the priority for this ticket. Ultimately, we want to have read replicas in different regions. In order to reduce the latency, we want to have “Standy” pageserver nearby

Don't we want the replica to be of a specific tenant?

yes, we need to replicate data per tenant

@LizardWizzard @hlinnaka before starting the deep dive discussion here, do we have this already partially covered for the read-only state for tenant relocation?

It depends on what is meant by HA. What are the requirements?


Tests failing when DEBUG flag is set

I believe some of the 34 failures are due to nil pointers that are only de-referenced when debugging code is called, e.g:
•! Panic in Spec Teardown (AfterEach) [0.114 seconds]
Session [AfterEach] timeouts doesn't time out when it just sent a packet
/usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session_test.go:1466

  Test Panicked
  runtime error: invalid memory address or nil pointer dereference
  /usr/lib/google-golang/src/runtime/panic.go:522

  Full Stack Trace
        /usr/lib/google-golang/src/runtime/panic.go:522 +0x1b5
  github.com/lucas-clemente/quic-go.(*session).logPacket(0xc00071a280, 0xc000a951d0)
        /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session.go:1291 +0x8b
  github.com/lucas-clemente/quic-go.(*session).sendConnectionClose(0xc00071a280, 0xc0005e9200, 0xc0005e9200, 0x126ef00)
        /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session.go:1282 +0xfa
  github.com/lucas-clemente/quic-go.(*session).handleCloseError(0xc00071a280, 0x0, 0x0, 0x100)
        /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session.go:1040 +0xbb
  github.com/lucas-clemente/quic-go.(*session).run(0xc00071a280, 0x0, 0x0)
        /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session.go:468 +0xb6c
  github.com/lucas-clemente/quic-go.glob..func<IP_ADDRESS>(0xc0004ee628, 0xc0004ee600)
        /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session_test.go:1474 +0x8a
  created by github.com/lucas-clemente/quic-go.glob..func22.15.6
        /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/session_test.go:1471 +0x140

But there's also this type of failure:
• Failure [0.002 seconds]
Server handling requests [It] handles a panicking handler
/usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/http3/server_test.go:143

  Unexpected call to *mockquic.MockStream.StreamID([]) at /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/internal/mocks/quic/stream.go:151 because: there are no expected calls of the method "StreamID" for that receiver

  /usr/local/google/home/tatianabradley/code/go/src/github.com/lucas-clemente/quic-go/internal/mocks/quic/stream.go:151

That makes sense. We're getting the stream ID just in order to log it, so there'll be an additional call to StreamID() of the mock stream.
So currently the unit tests runnable in DEBUG mode. Probably we just need to initialize an utils.DefaultLogger to fix the nil pointer dereferences, and add a few mock calls (this is the annoying part about it, since we don't really want to test our logging behavior).


PEP 541: Transfer ownership of unmaintained pyfit

I am unable to reach the maintainer for PyFIT, as the email<EMAIL_ADDRESS>bounced back stating it doesn't exist. The package was last updated over 10 years ago. There does not appear to be a GitHub repository associated with the project. Therefore, it can be considered abandoned according to the guidelines. Can someone please transfer ownership to me for use in my project?
https://pypi.org/project/PyFIT/
Referencing issue
https://github.com/pypa/warehouse/issues/1506
Abandonment criteria met:

owner not reachable (see Reachability above);
no releases within the past twelve months; and
no activity from the owner on the project's home page (or no home page listed).

An abandoned project can be transferred to a new owner for purposes of reusing the name when ALL of the following are met:

the project has been determined abandoned by the rules described above;
the candidate is able to demonstrate their own failed attempts to contact the existing owner;
the candidate is able to demonstrate that the project suggested to reuse the name already exists and meets notability requirements;
the candidate is able to demonstrate why a fork under a different name is not an acceptable workaround;
download statistics on the Package Index for the existing package indicate project is not being used; and
the maintainers of the Package Index don't have any additional reservations.

I can confirm the abandonment criteria. I am unable to reach the maintainer at the address in the PyPI database or the setup.py (both bounce), or locate a GitHub user that seems to be the same. There are complaints of abandonment and the inability to install dating back to 2008. In 2013, someone with the same name as the PyPI maintainer posted to the official mailing list that they no longer support PyFIT.
It appears to get a handful (<10) daily downloads; it does not work on Python 3.
I think that leaves two criteria:

the candidate is able to demonstrate that the project suggested to reuse the name already exists and meets notability requirements;
the candidate is able to demonstrate why a fork under a different name is not an acceptable workaround;

Can you address those points please?