Accept more variations on inputs when parsing a string

Problem
At the moment we support these input variations (7 in total), plus that we trim leading and trailing whitespace:
10 digit string

YYMMDD-BBBC
YYMMDD+BBBC
YYMMDD BBBC (Treated as YYMMDD-BBBC)
YYMMDDBBBC (Treated as YYMMDD-BBBC)

12 digit string

YYYYMMDDBBBC
YYYYMMDD-BBBC (Treated as YYYYMMDDBBBC)
YYYYMMDD BBBC (Treated as YYYYMMDDBBBC)

Though, after some offline discussions with @jgbptl (who has implemented this before), I've realized users are writing personal identity numbers in far more format than these. Just a few examples:

YYYY-MM-DD-BBBC
YYMMDD.BBBC
YYMMDD  BBBC (two whitespaces)

Suggestion
I'd vote for expanding the variations we allow for input, while still having the possibility to parse in a more strict mode (as we have now). Ideally adding support for more variations could be done in a none breaking way so that we can release it as (something like) 1.1.0.
We should accept pretty much any character and just strip it away, while still handling the + sign in the 10 digit version as a special case. Because we have the checksum, we can be very confident that we actually are parsing a valid PIN.
Solution
The pseudo code for how to parse basically all versions would be:

Strip out all chars except numbers (0-9) and plus (+).
If the value now ends with +XXXX (where X is a digit), treat the delimiter as plus (+), otherwise hyphen (-).
Strip out all remaining plus (+) chars.
If the length is 12 chars, don't care about the delimiter and instead parse it as a full year.
If the length is 10 chars. parse it and take the delimiter into account.

My proposed solution is to follow roughly how DateTime does this:
https://docs.microsoft.com/en-us/dotnet/api/system.globalization.datetimestyles?view=netstandard-2.0
In our case it would mean adding overloads to the .Parse(), .ParseInSpecificYear(), .TryParse() and .TryParseInSpecificYear() that would accept an SwedishPersonalidentityNumberStyles that would specify  some rules for what to parse. Either we do it exactly as they do, with bitflags, but I think an enum could be enough, with these three values:

SwedishPersonalidentityNumberStyles.Strict (Would only allow the strictly correct versions, YYYYMMDDBBBC, YYMMDD-BBBC and YYMMDD+BBBC. No trimming of white space etc.)
SwedishPersonalidentityNumberStyles.Default (Would work as of today, trim leading and trailing white space and supporting the 7 versions described above).
SwedishPersonalidentityNumberStyles.Loose (Would try the best it can to actually parse it, basically removing all invalid chars etc.)

If not specified, SwedishPersonalidentityNumberStyles.Default would be used.
So, what do you think? Good approach and what should we name things?

Sounds good to me. When we go to v2 maybe we can consider making "Loose" the default, but since we do not want a breaking change for v1.1.0 we need to keep the same defaults as we have today.

I've now updated the original issue with pseudo code for how a "loose" parsing implementation could look like.

I've also been thinking, and actually think we should aim for the bitwise flags instead of enum. It has multiple advantages, such as:

Allows us to introduce new rules without making a breaking change.
Allows the consumer to more precise define allowed formats, if they (for some reason) would like to limit possible variations.
Allows for more consistency over time as the consumer can precisely define what rules to apply for a consistent parsing result over time and versions of the lib.

Examples of such flags would be:

AllowWhiteSpaces
AllowAnyChar

So from your pseudocode what we actually have to do is just 1.
Then we can send the resulting string to our current parser and it will just work.
With one caveat, I am not sure how a 12 digit number with a plus delimiter is handled maybe a small fix is required here.

We should consider if this is best handled by “cleaning” the input string according to the provide style and then passing it to the parser.
Or if it should be handled with branching in the parser, e.g. we build up or select the regex pattern depending on the selected styles.

So from your pseudocode what we actually have to do is just 1.

Nah, there might still be pluses earlier in the value, like (extreme case) 12+82+01+01-1234, so we would do  the check in no 2 as well, right?

We should consider if this is best handled by “cleaning” the input string according to the selected style and then passing it to the parser.

I think it can still be part of the internal parser, but I like the idea of pre-processing (cleaning) so that once we reach the Regexp, we have a cleaned input.

I’m thinking that maybe we should be a little YAGNI here and only add support for “Loose” parsing (since it can be done quite easily).

Yes, after giving this some more thought, I'm ready to agree :) We will have to step to 2.0, but here is my plan to make this relevant:
As we are planning on supporting SwedishCompanyRegistrationNumber (which is very similar in how it works) we should have a very similar parsing mechanism, cleaning the value in the same way etc. It would be natural for us to share some logics for this and release it as 2.0.
Thoughts?

I may be derailing the conversation a bit here, feel free to move this to another issue ;)
Regarding the SwedishCompanyRegistrationNumber (and the other numbers) have we given any thought to what the API would look like? In another project where we worked with identity numbers our problem was that we had an identitfier but did not know what type it was, so we just called the parser with the string and if it was a personal number we got a personal number back, if it was an company registration number we got an organisation number and so on.
That was implemented with just one parser with 3 or 4 different regex patterns. So I think there will be very muched shared code. In fact very little code that is not shared.
On that note I almost would expect us to instead of having SwedishPersonalIdentityNumber there would just be a SwedishIdentityNumber class with a Parse-method that can handle all types of numbers and will return the correct type.
So then SwedishPersonalIdentityNumber and SwedishCompanyRegistrationNumber and SwedishCoordinationNumber would just be facades using one and the same parser. So all parsing code would essentially be shared.
Then you can choose to use the full parser if you want to parse any type of number or pick one of the specific ones if you want to just parse SwedishPersonalIdentityNumber for example.

Nah, there might still be pluses earlier in the value, like (extreme case) 12+82+01+01-1234, so we would do the check in no 2 as well, right?

You are right, but in that case I prefer to handle that in the regex with optional matches for any character <.> or even <.*> instead of doing multiple cleaning passes over the input string.
@"((?<fullYear>[0-9]{4})|(?<shortYear>[0-9]{2})).*(?<month>[0-9]{2}).*(?<day>[0-9]{2}).*"

Or to be more clear: I rather we do not split the parsing logic into two different parts of the code. Either we use regex (which is what we have now) or we do all the work "manually" with string manipulation.
I do not necessarily think that regex is the best way, but it works fine for now, but it can get ugly if the patterns gets too complex.


RNAlib not installed error on Python3.10

Hello,
I've encountered an error of "ViennaRNA / RNAlib not installed" when I import the ViennaRNA module. But, installing it on Python3.9 works well.
What can be a problem?
My system configuration is

Thanks in advance!

I'm sorry, are you saying that when you install ViennaRNA from PyPI using pip install ViennaRNA on python=3.9 on your MacOS system, it works (you are able to import the library), but not when you install it a python=3.10 environment? Are you using a conda environment for this? What about `python=3.11'?

I'm working on conda environment for it, and on python=3.9, it works like a charm.
But, for python=3.10, the system logs
Collecting ViennaRNA
  Using cached ViennaRNA-2.5.0a5-py3-none-any.whl
Installing collected packages: ViennaRNA
Successfully installed ViennaRNA-2.5.0a5

Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 19:01:19) [Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import ViennaRNA
Traceback (most recent call last):
  File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.10/site-packages/ViennaRNA/__init__.py", line 2, in <module>
    import RNA
ModuleNotFoundError: No module named 'RNA'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.10/site-packages/ViennaRNA/__init__.py", line 4, in <module>
    raise ImportError(' ViennaRNA / RNAlib not installed')
ImportError:  ViennaRNA / RNAlib not installed
>>>

About python=3.11,
Collecting ViennaRNA
  Using cached ViennaRNA-2.5.0a5.tar.gz (58.0 MB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: ViennaRNA
  Building wheel for ViennaRNA (setup.py): started
  Building wheel for ViennaRNA (setup.py): still running...
  Building wheel for ViennaRNA (setup.py): still running...
  Building wheel for ViennaRNA (setup.py): finished with status 'error'
  Running setup.py clean for ViennaRNA
Failed to build ViennaRNA
Installing collected packages: ViennaRNA
  Running setup.py install for ViennaRNA: started
  Running setup.py install for ViennaRNA: finished with status 'error'

      config.status: executing depfiles commands
      config.status: executing libtool commands
      configure:

      ======================================
          ViennaRNA Package 2.5.0
      ======================================

      Successfully configured with the following options:

      Sub Packages
      ------------
        * Kinfold                   : no
        * RNAforester               : no
        * Analyse{Dists,Seqs}       : no
        * RNAlocmin                 : no
        * Kinwalker                 : no

      Extra Libraries
      ---------------
        * Support Vector Machine    : yes
        * GNU Scientific Library    : no
        * GNU MPFR                  : no
        * JSON                      : yes

      Features
      --------
        * Use hash for NR Sampling  : no
        * C11 features              : yes
        * TTY colors                : yes
        * Float Precision(PF}       : no
        * Deprecation Warnings      : no

      Optimizations
      -------------
        * Auto Vectorization        : yes
        * Explicit SIMD Extension   : yes
        * Link Time Optimization    : no
        * POSIX Threads             : yes
        * OpenMP                    : no

      Scripting Language Interfaces
      -----------------------------
        * Perl 5                    : no
        * Python 3.x                : yes
        * Python 2.x                : yes

      Documentation
      -------------
        * Reference Manual (PDF)    : no
        * Reference Manual (HTML)   : no
        * Tutorial (PDF)            : no
        * Tutorial (HTML)           : no
        * CLA (PDF)                 : no

      Unit Tests
      ----------
        * Executable Programs       : yes
        * C-Library                 : no
        * Perl 5 Interface          : no
        * Python 3.x Interface      : yes
        * Python 2.x Interface      : yes

      MacOS X
      -------
        * Universal Binary          : no
        * Installer                 : no
        * SDK                       : custom

      Install Directories
      -------------------
        * Executables               : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/bin
        * Libraries                 : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/lib
        * Header files              : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/include
        * Extra Data                : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/share
        * Man pages                 : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/share/man
        * Documentation             : Not to be installed
            (HTML)                  :
            (PDF)                   :
        * Perl5 Interface           : Not to be installed
            (binaries)              :
            (scripts)               :
        * Python 3.x Interface      :
            (binaries)              : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
            (scripts)               : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
        * Python 2.x Interface      :
            (binaries)              : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/lib/python2.7/site-packages
            (scripts)               : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/lib/python2.7/site-packages

      You can run 'make', 'make check', and 'make install' now!
      /Library/Developer/CommandLineTools/usr/bin/make  all-recursive
      Making all in src
      Making all in ViennaRNA
      Making all in static
      /Library/Developer/CommandLineTools/usr/bin/make  all-am
      make[5]: Nothing to be done for `all-am'.
          Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
              vsprintf(buf,fmt,ap);
              ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here
      __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
      ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
              #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                            ^
      1 warning generated.
        CC       ../json/json.lo
        CC       alphabet.lo
        CC       sequence.lo
        CC       unstructured_domains.lo
        CC       grammar.lo
        CC       heat_capacity.lo
        CC       zscore.lo
        CC       libRNA_concentrations_la-concentrations.lo
        CXX      ../dlib-19.22/dlib/all/libRNA_concentrations_la-source.lo
        CXX      libRNA_concentrations_la-wrap_dlib.lo
        CXXLD    libRNA_concentrations.la
        CC       constraints/constraints.lo
        CC       constraints/SHAPE.lo
        CC       constraints/hard.lo
        CC       constraints/soft.lo
        CC       constraints/ligand.lo
        CCLD     libRNA_constraints.la
        CC       datastructures/basic_datastructures.lo
        CC       datastructures/lists.lo
        CC       datastructures/char_stream.lo
        CC       datastructures/stream_output.lo
        CC       datastructures/hash_tables.lo
      datastructures/hash_tables.c:339:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
        k   = ((vrna_ht_entry_db_t *)x)->structure;
            ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      datastructures/hash_tables.c:340:39: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
        len = length = (unsigned int)strlen(k);
                                            ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/string.h:82:28: note: passing argument to parameter '__s' here
      size_t   strlen(const char *__s);
                                  ^
      2 warnings generated.
        CC       datastructures/heap.lo
        CCLD     libRNA_datastructures.la
        CC       utils/utils.lo
        CC       utils/string_utils.lo
        CC       utils/structure_utils.lo
        CC       utils/structure_tree.lo
        CC       utils/msa_utils.lo
        CC       utils/higher_order_functions.lo
        CC       utils/cpu.lo
        CC       utils/units.lo
        CC       io/io_utils.lo
        CC       io/file_formats.lo
        CC       io/file_formats_msa.lo
        CC       search/BoyerMoore.lo
        CC       commands.lo
        CC       combinatorics.lo
        CC       utils/svm_utils.lo
        CCLD     libRNA_utils.la
        CC       plotting/alignments.lo
        CC       plotting/layouts.lo
        CC       plotting/probabilities.lo
        CC       plotting/structures.lo
        CC       plotting/plot_utils.lo
        CC       plotting/naview.lo
        CC       plotting/RNApuzzler/RNApuzzler.lo
      In file included from plotting/RNApuzzler/RNApuzzler.c:20:
      In file included from plotting/RNApuzzler/includes/resolveIntersections.inc:15:
      plotting/RNApuzzler/includes/handleAncestorIntersections.inc:64:11: warning: 10 enumeration values not handled in switch: 'noIntersection', 'LxL', 'LxS'... [-Wswitch]
        switch (it) {
                ^~
      plotting/RNApuzzler/includes/handleAncestorIntersections.inc:64:11: note: add missing switch cases
        switch (it) {
                ^
      1 warning generated.

        CCLD     RNAalifold
        CC       RNAplfold_cmdl.o
        CC       RNAplfold.o
        CCLD     RNAplfold
        CC       RNAup_cmdl.o
        CC       RNAup.o
        CCLD     RNAup
        CC       RNAaliduplex_cmdl.o
        CC       RNAaliduplex.o
        CCLD     RNAaliduplex
        CC       RNALalifold_cmdl.o
        CC       RNALalifold.o
        CCLD     RNALalifold
        CC       RNA2Dfold_cmdl.o
        CC       RNA2Dfold.o
        CCLD     RNA2Dfold
        CC       RNAparconv_cmdl.o
        CC       RNAparconv.o
        CCLD     RNAparconv
        CC       RNAPKplex_cmdl.o
        CC       RNAPKplex.o
        CCLD     RNAPKplex
        CC       RNAplex_cmdl.o
        CC       RNAplex.o
      RNAplex.c:2083:46: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source]
        if (sscanf(names[0], "%255[^/]/%lld-%lld", bla, &begin, &end) == 3) /* initialize location_flag; */
                                                   ^
      RNAplex.c:2099:48: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source]
          if (sscanf(names[i], "%255[^/]/%lld-%lld", bla, &begin, &end) == 3) {
                                                     ^
      2 warnings generated.
        CCLD     RNAplex
        CC       RNAsnoop_cmdl.o
        CC       RNAsnoop.o
        CCLD     RNAsnoop
        CC       RNApvmin_cmdl.o
        CC       RNApvmin.o
        CCLD     RNApvmin
        CC       RNAdos_cmdl.o
        CC       RNAdos.o
        CCLD     RNAdos
        CC       RNAmultifold_cmdl.o
        CC       RNAmultifold.o
        CCLD     RNAmultifold
      Making all in Utils
        CC       b2ct.o
        CCLD     b2ct
        CC       popt.o
        CCLD     popt
        CC       ct2db_cmdl.o
        CC       ct2db.o
        CCLD     ct2db
      make[3]: Nothing to be done for `all-am'.
      Making all in man
      make[2]: Nothing to be done for `all'.
      Making all in misc
      make[2]: Nothing to be done for `all'.
      Making all in doc
      Making all in CLA
      make[3]: Nothing to be done for `all'.
      make[3]: Nothing to be done for `all-am'.
      Making all in RNA-Tutorial
      make[2]: Nothing to be done for `all'.
      Making all in interfaces
      Making all in Python
        CXX      _RNA_la-RNA_wrap.lo
      RNA_wrap.cpp:4693:11: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                sprintf(msg, "attempt to assign sequence of size %lu to extended slice of size %lu", (unsigned long)is.size(), (unsigned long)replacecount);
                ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
      __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
      ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
              #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                            ^
      RNA_wrap.cpp:4709:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
              sprintf(msg, "attempt to assign sequence of size %lu to extended slice of size %lu", (unsigned long)is.size(), (unsigned long)replacecount);
              ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
      __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
      ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
              #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                            ^
      RNA_wrap.cpp:5049:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
              sprintf(msg, "in sequence element %d ", (int)_index);
              ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
      __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
      ^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
              #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                            ^
      3 warnings generated.
        CXXLD    _RNA.la
        GEN      RNA/__init__.py
        GEN      RNA/_RNANone
        GEN      RNA/__pycache__/__init__.cpython-311.pyc
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
      ModuleNotFoundError: No module named '_RNA'
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py", line 11, in <module>
          from . import _RNA
      ImportError: cannot import name '_RNA' from partially initialized module 'RNA' (most likely due to a circular import) (/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py)
      make[3]: *** [RNA/__pycache__/__init__.cpython-311.pyc] Error 1
      make[2]: *** [all-recursive] Error 1
      make[1]: *** [all-recursive] Error 1
      make: *** [all] Error 2
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 110, in <module>
          setup(
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/dist.py", line 1208, in run_command
          super().run_command(command)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 360, in run
          self.run_command("install")
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/dist.py", line 1208, in run_command
          super().run_command(command)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 107, in run
          self.compile_and_install_ViennaRNA()
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 98, in compile_and_install_ViennaRNA
          subprocess.check_call('make', cwd=src_path, shell=True)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for ViennaRNA
  error: subprocess-exited-with-error

  × Running setup.py install for ViennaRNA did not run successfully.
  │ exit code: 1
  ╰─> [473 lines of output]
      running install
      /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated.  /Library/Developer/CommandLineTools/usr/bin/ld
      checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
      checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
      checking the name lister (/usr/bin/nm -B) interface... BSD nm
      checking the maximum length of command line arguments... 786432
      checking how to convert aarch64-apple-darwin22.4.0 file names to aarch64-apple-darwin22.4.0 format... func_convert_file_noop
      checking how to convert aarch64-apple-darwin22.4.0 file names to toolchain format... func_convert_file_noop
      checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
      checking for objdump... objdump
      checking how to recognize dependent libraries... pass_all
      checking for dlltool... no
      checking how to associate runtime and link libraries... printf %s\n
      checking for archiver @FILE support... no
      checking for strip... strip
      checking for ranlib... ranlib
      checking command to parse /usr/bin/nm -B output from gcc object... ok
      checking for sysroot... no
      checking for a working dd... /bin/dd
      checking how to truncate binary pipes... /bin/dd bs=4096 count=1
      checking for mt... no
      checking if : is a manifest tool... no
      checking for dsymutil... dsymutil
      checking for nmedit... nmedit
      checking for lipo... lipo
      checking for otool... otool
      checking for otool64... no
      checking for -single_module linker flag... yes
      checking for -exported_symbols_list linker flag... yes
      checking for -force_load linker flag... yes
      checking for dlfcn.h... yes
      checking for objdir... .libs
      checking if gcc supports -fno-rtti -fno-exceptions... yes
      checking for gcc option to produce PIC... -fno-common -DPIC
      checking if gcc PIC flag -fno-common -DPIC works... yes
      checking if gcc static flag -static works... no
      checking if gcc supports -c -o file.o... yes
      checking if gcc supports -c -o file.o... (cached) yes
      checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
      checking dynamic linker characteristics... darwin22.4.0 dyld
      checking how to hardcode library paths into programs... immediate
      checking whether stripping libraries is possible... yes
      checking if libtool supports shared libraries... yes
      checking whether to build shared libraries... yes
      checking whether to build static libraries... yes
      checking how to run the C++ preprocessor... g++ -E
      checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld
      checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
      checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
      checking for g++ option to produce PIC... -fno-common -DPIC
      checking if g++ PIC flag -fno-common -DPIC works... yes
      checking if g++ static flag -static works... no
      checking if g++ supports -c -o file.o... yes
      checking if g++ supports -c -o file.o... (cached) yes
      checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
      checking dynamic linker characteristics... darwin22.4.0 dyld
      checking how to hardcode library paths into programs... immediate
      checking for exp in -lm... yes
      ./configure: line 19003: #include: command not found
      checking for egrep... (cached) /usr/bin/grep -E
      checking for _Bool... yes
      checking for stdbool.h that conforms to C99... yes
      checking for malloc.h... no
      checking for float.h... yes
      checking for limits.h... yes
      checking for stdlib.h... (cached) yes
      checking for string.h... (cached) yes
      checking for strings.h... (cached) yes
      checking for unistd.h... (cached) yes
      checking for math.h... yes
      checking for stdarg.h... yes
      checking for GNU libc compatible malloc... yes
      checking for GNU libc compatible realloc... yes
      checking for working strtod... yes
      checking for floor... yes
      checking for strdup... yes
      checking for strstr... yes
      checking for strchr... yes
      checking for strrchr... yes
      checking for strstr... (cached) yes
      checking for strtol... yes
      checking for strtoul... yes
      checking for pow... yes
      checking for rint... yes
      checking for sqrt... yes
      checking for erand48... yes
      checking for memset... yes
      checking for memmove... yes
      checking for erand48... (cached) yes
      checking for asprintf... yes
      checking for vasprintf... yes
      checking for an ANSI C-conforming const... yes
      checking for size_t... yes
      checking for inline... inline
      checking for pdflatex... no
      checking for bibtex... no
      checking for makeindex... no
      checking for pkg-config... /opt/homebrew/bin/pkg-config
      checking pkg-config is at least version 0.9.0... yes
      checking for C compiler vendor... clang
      checking for perl... /opt/homebrew/bin/perl
      checking whether C compiler accepts -fno-strict-aliasing... yes
      checking whether C++ compiler accepts -fno-strict-aliasing... yes
      checking whether the linker accepts -fno-strict-aliasing... yes
      checking whether the C compiler allows unnamed unions of unnamed structs... yes
      checking whether the C++ compiler allows unnamed unions of unnamed structs... yes
      checking whether C compiler accepts -flto... yes
      checking whether C++ compiler accepts -flto... yes
      checking whether C compiler accepts -ffat-lto-objects... yes
      checking whether C++ compiler accepts -ffat-lto-objects... yes
      configure: WARNING: Trying to re-set ar/ranlib/nm to compiler specific wrappers
      configure: WARNING: Building for OS X
      checking whether the linker supports Link time Optimization (LTO)... no
      configure: WARNING: Your linker does not support Link Time Optimizaton! Disabling LTO support!
      configure: WARNING: Your compiler/linker combination does not support link-time optimization (LTO)
      checking for ./src/libsvm-3.25/svm.cpp... yes
      checking for ./src/libsvm-3.25/svm.h... yes
      checking for ./src/json/json.c... yes
      checking for ./src/json/json.h... yes
      checking for cblas_dgemm in -lgslcblas... no
      checking for gsl_blas_dgemm in -lgsl... no
      configure: WARNING: "Can't find libgsl. Falling back to default implementation."
      checking whether gcc is Clang... yes
      checking whether pthreads work with "-pthread" and "-lpthread"... yes
      checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no
      checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
      checking whether more special flags are required for pthreads... no
      checking for PTHREAD_PRIO_INHERIT... yes
      checking compiler support for AVX 512 instructions... no
      checking compiler support for SSE 4.1 instructions... no
      checking whether C compiler accepts -ftree-vectorize... yes
      checking for mpfr.h... no
      configure: WARNING:
      ==========================
      Failed to find mpfr.h!

      You probably need to install the mpfr-devel package or similar
      ==========================

      checking for ./interfaces/Makefile.am... yes
      checking for swig... no
      checking for swig2.0... no
      checking for ./interfaces/Python2/Makefile.am... yes
      checking for ./interfaces/Python2/RNA_wrap.cpp... yes
      checking for ./interfaces/Python2/RNA.py... yes
      checking for python2... /Library/Frameworks/Python.framework/Versions/2.7/bin/python2
      checking for Python2 include path... /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
      checking for /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h... yes
      checking for Python2 ldflags... -bundle -undefined dynamic_lookup
      checking for Python2 extension linker... gcc -bundle -undefined dynamic_lookup -arch x86_64 -g
      checking for directory to install Python2 scripts in... ${prefix}/lib/python2.7/site-packages
      checking for directory to install architecture dependent python2 things in... ${exec_prefix}/lib/python2.7/site-packages
      checking for Python2 module extension... .so
      checking for ./interfaces/Python/Makefile.am... yes
      checking for ./interfaces/Python/RNA_wrap.cpp... yes
      checking for ./interfaces/Python/RNA.py... yes
      checking for python3... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/bin/python3
      checking for Python3 include path... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/include/python3.11
      checking for /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/include/python3.11/Python.h... yes
      checking for Python3 ldflags... -bundle -undefined dynamic_lookup
      checking for Python3 extension linker... clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib -L/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib -Wl,-rpath,/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib -L/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib
      checking for directory to install Python3 scripts in... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
      checking for directory to install architecture dependent python3 things in... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
      checking for Python3 module extension... None
      checking for Python3 tag for cached compiled scripts... cpython-311
      checking for Python3 extension of cached and optimized bytecode... cpython-311.opt-1.pyc
      checking for doxygen... no
      checking for dot... no
      checking for egrep... /usr/bin/egrep
      checking for perl... /opt/homebrew/bin/perl
      checking for htlatex... no
      checking for CHECK... no
      configure: WARNING: check not found -- will not build C-library Unit tests
      checking for diff... /usr/bin/diff
      checking for xxd... /usr/bin/xxd
      checking for gengetopt... no
      checking for help2man... no
      checking whether g++ supports C++11 features with -std=c++11... yes
      checking for ./src/dlib-19.22/dlib/all/source.cpp... yes
      checking that generated files are newer than configure... done
      configure: creating ./config.status
      config.status: creating packaging/macosx/Makefile
      config.status: creating packaging/macosx/Distribution.xml
      config.status: creating packaging/macosx/resources/welcome.txt
      config.status: creating interfaces/Python2/Makefile
      config.status: creating interfaces/Python2/version.i
      config.status: creating interfaces/Python/Makefile
      config.status: creating interfaces/Python/version.i
      config.status: creating tests/Makefile
      config.status: creating tests/RNApath.py
      config.status: creating tests/RNAHelpers.pm
      config.status: creating tests/test-env.sh
      config.status: creating src/ViennaRNA/static/templates_postscript.h
      config.status: creating src/ViennaRNA/static/templates_svg.h
      config.status: creating src/ViennaRNA/static/energy_parameter_sets.h
      config.status: creating src/ViennaRNA/vrna_config.h
      config.status: creating misc/Makefile
      config.status: creating interfaces/Makefile
      config.status: creating Makefile
      config.status: creating RNAlib2.pc
      config.status: creating src/Utils/Makefile
      config.status: creating src/bin/Makefile
      config.status: creating src/Makefile
      config.status: creating src/ViennaRNA/Makefile
      config.status: creating src/ViennaRNA/static/Makefile
      config.status: creating man/Makefile
      config.status: creating doc/Makefile
      config.status: creating doc/CLA/Makefile
      config.status: creating RNA-Tutorial/Makefile
      config.status: creating man/cmdlopt.sh
      config.status: creating examples/Makefile
      config.status: creating packaging/viennarna.spec
      config.status: creating packaging/PKGBUILD
      config.status: creating packaging/win_installer_archlinux_i686.nsi
      config.status: creating packaging/win_installer_archlinux_x86_64.nsi
      config.status: creating packaging/win_installer_fedora_i686.nsi
      config.status: creating packaging/win_installer_fedora_x86_64.nsi
      config.status: creating config.h
      config.status: config.h is unchanged
      config.status: executing depfiles commands
      config.status: executing libtool commands
      configure:

      ======================================
          ViennaRNA Package 2.5.0
      ======================================

      Successfully configured with the following options:

      Sub Packages
      ------------
        * Kinfold                   : no
        * RNAforester               : no
        * Analyse{Dists,Seqs}       : no
        * RNAlocmin                 : no
        * Kinwalker                 : no

      Extra Libraries
      ---------------
        * Support Vector Machine    : yes
        * GNU Scientific Library    : no
        * GNU MPFR                  : no
        * JSON                      : yes

      Features
      --------
        * Use hash for NR Sampling  : no
        * C11 features              : yes
        * TTY colors                : yes
        * Float Precision(PF}       : no
        * Deprecation Warnings      : no

      Optimizations
      -------------
        * Auto Vectorization        : yes
        * Explicit SIMD Extension   : yes
        * Link Time Optimization    : no
        * POSIX Threads             : yes
        * OpenMP                    : no

      Scripting Language Interfaces
      -----------------------------
        * Perl 5                    : no
        * Python 3.x                : yes
        * Python 2.x                : yes

      Documentation
      -------------
        * Reference Manual (PDF)    : no
        * Reference Manual (HTML)   : no
        * Tutorial (PDF)            : no
        * Tutorial (HTML)           : no
        * CLA (PDF)                 : no

      Unit Tests
      ----------
        * Executable Programs       : yes
        * C-Library                 : no
        * Perl 5 Interface          : no
        * Python 3.x Interface      : yes
        * Python 2.x Interface      : yes

      MacOS X
      -------
        * Universal Binary          : no
        * Installer                 : no
        * SDK                       : custom

      Install Directories
      -------------------
        * Executables               : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/bin
        * Libraries                 : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/lib
        * Header files              : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/include
        * Extra Data                : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/share
        * Man pages                 : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/share/man
        * Documentation             : Not to be installed
            (HTML)                  :
            (PDF)                   :
        * Perl5 Interface           : Not to be installed
            (binaries)              :
            (scripts)               :
        * Python 3.x Interface      :
            (binaries)              : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
            (scripts)               : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
        * Python 2.x Interface      :
            (binaries)              : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/lib/python2.7/site-packages
            (scripts)               : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/lib/python2.7/site-packages

      You can run 'make', 'make check', and 'make install' now!
      /Library/Developer/CommandLineTools/usr/bin/make  all-recursive
      Making all in src
      Making all in ViennaRNA
      Making all in static
      /Library/Developer/CommandLineTools/usr/bin/make  all-am
      make[5]: Nothing to be done for `all-am'.
        CC       plotting/alignments.lo
        CC       plotting/probabilities.lo
        CC       plotting/structures.lo
        CCLD     libRNA_plotting.la
        CC       params/io.lo
        CCLD     libRNA_params.la
        CXXLD    libRNA_conv.la
        CXXLD    libRNA.la
        GEN      libRNA.a
      Making all in bin
        CCLD     RNAfold
        CCLD     RNAeval
        CCLD     RNAheat
        CCLD     RNApdist
        CCLD     RNAdistance
        CCLD     RNAinverse
        CCLD     RNAplot
        CCLD     RNAsubopt
        CCLD     RNALfold
        CCLD     RNAcofold
        CCLD     RNApaln
        CCLD     RNAduplex
        CCLD     RNAalifold
        CCLD     RNAplfold
        CCLD     RNAup
        CCLD     RNAaliduplex
        CCLD     RNALalifold
        CCLD     RNA2Dfold
        CCLD     RNAparconv
        CCLD     RNAPKplex
        CCLD     RNAplex
        CCLD     RNAsnoop
        CCLD     RNApvmin
        CCLD     RNAdos
        CCLD     RNAmultifold
      Making all in Utils
        CCLD     b2ct
        CCLD     popt
        CCLD     ct2db
      make[3]: Nothing to be done for `all-am'.
      Making all in man
      make[2]: Nothing to be done for `all'.
      Making all in misc
      make[2]: Nothing to be done for `all'.
      Making all in doc
      Making all in CLA
      make[3]: Nothing to be done for `all'.
      make[3]: Nothing to be done for `all-am'.
      Making all in RNA-Tutorial
      make[2]: Nothing to be done for `all'.
      Making all in interfaces
      Making all in Python
        CXXLD    _RNA.la
        GEN      RNA/_RNANone
        GEN      RNA/__pycache__/__init__.cpython-311.pyc
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
      ModuleNotFoundError: No module named '_RNA'
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py", line 11, in <module>
          from . import _RNA
      ImportError: cannot import name '_RNA' from partially initialized module 'RNA' (most likely due to a circular import) (/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py)
      make[3]: *** [RNA/__pycache__/__init__.cpython-311.pyc] Error 1
      make[2]: *** [all-recursive] Error 1
      make[1]: *** [all-recursive] Error 1
      make: *** [all] Error 2
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 110, in <module>
          setup(
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/dist.py", line 1208, in run_command
          super().run_command(command)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 107, in run
          self.compile_and_install_ViennaRNA()
        File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 98, in compile_and_install_ViennaRNA
          subprocess.check_call('make', cwd=src_path, shell=True)
        File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> ViennaRNA

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Thanks:)

I am also getting the same issue.
The main important log seems to be here (for python 3.11):
ImportError: cannot import name '_RNA' from partially initialized module 'RNA' (most likely due to a circular import) (/tmp/pip-install-87uhvbpu/viennarna_0d07ead04835461f97ab19d1df6217c4/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py)```

Please try installing again now. The problems should now have been fixed.

Works for me with 2.6.2. Thanks! I guess that this can be closed for now.


Doesn't work with db2

This doesn't work with db2 because of the dependency on ssb-backlinks.  According to @arj03:

The purge module needs to be converted to db2. Meaning backlinks should be replaced with a seek query. Probably a prefix query (like key).

(From here: https://github.com/arj03/ssb-browser-demo/issues/8#issuecomment-761753817)
Unfortunately, I feel like having looked at the code involved, I think it's beyond my capabilities to fix this.  So I'm hoping maybe filing this issue will help highlight the problem.  Because if this can be fixed, then I'm fairly certain I can make this work:
https://github.com/arj03/ssb-browser-demo/issues/8

I'll work on this, no worries

I'll work on this, no worries

Awesome.  Thanks!  Sorry about the lack of help on this, but I'm pretty sure I'd make more of a mess than what I'd fix on this one.

Awesome.  Thanks!  Sorry about the lack of help on this, but I'm pretty sure I'd make more of a mess than what I'd fix on this one.

Works now with 1.0.0

Works now with 1.0.0


Nvidia power management configuration

Looking through the repository, none of the configurations have hardware.nvidia.powerManagement configured. On my dell machine,  I've been able several watts with;
  hardware.nvidia = {
    powerManagement = {
      enable = true;
      finegrained = true;
    };
    nvidiaPersistenced = true;
  };

These options control these things from the arch wiki: https://wiki.archlinux.org/title/PRIME#PCI-Express_Runtime_D3_(RTD3)_Power_Management
I'm wondering if not including this configuration is intentional or not? I'm not sure if this counts as an opinionated setting.
If it is okay I would like to submit a pr for my machine.

I don't think this is intentional, at least I am not aware of that. Could be added here? https://github.com/NixOS/nixos-hardware/blob/2a7063461c3751d83869a2a0a8ebc59e34bec5b2/common/gpu/nvidia.nix#L19

From reading the nvidia docs it seems there is less to configure that I thought. The configuration is dependent on the microarchitecture.
For cards earlier than turing (below 20 series) there is no power saving and the configuration should be:
  hardware.nvidia = {
    powerManagement = {
      enable = true;
    };
  };

For turing (20 series) cards it should be:
  hardware.nvidia = {
   powerManagement = {
     enable = true;
     finegrained = true;
   };
   nvidiaPersistenced = true;
 };

and for ampere (30 series) and later cards power saving is enabled by default so it is just:
  hardware.nvidia = {
    powerManagement = {
      enable = true;
    };
  };

I'm not 100% sure on this and I only have my laptop to test but I think they are right.
So maybe its best set   hardware.nvidia.powerManagement.enable = true; is in
https://github.com/NixOS/nixos-hardware/blob/2a7063461c3751d83869a2a0a8ebc59e34bec5b2/common/gpu/nvidia.nix#L19
and for laptops with turing cards we can enable the other things in their configuration?

There could be a subprofile for turing cards that is more specific.

Yeah I do.

Should I submit a pr with another file in the gpu folder with the turing configuration and add the enable the powerManagement option in the nvidia file?


Use custom shaders by exposing shader handles?

hey, I wanted to add an animated effect to the outlines which involved changing its thickness on a per-vertex basis.
this involved copy and pasting the OUTLINE_SHADER_HANDLE into load_internal_asset! in order to overwrite the built-in shader with a new one. which is a bit hacky.
would it be possible to make OUTLINE_SHADER_HANDLE and FRAGMENT_SHADER_HANDLE public? or is there another way I should be doing this? thanks.

Hi, sorry I took so long to respond to this. I wasn't sure what to think at first. However, after some consideration, I conclude that the interface between the shader and the library is an implementation detail which is subject to change at any time. Hence, the handle ID is private. Copying the handle ID into your program may work, but the fact that it feels hacky should remind you that it may break in any future release.
I think the right way to do this is to maintain a vendor fork with this feature added.


spanner: confusing doc comment about iterators

Stop terminates the iteration. It should be called after every iteration.

https://godoc.org/cloud.google.com/go/spanner
Shouldn't it be called when you want to stop iterating, rather than after every iteration?
/cc @jba

@jba can you have a pass at this? Is this really a bug?

Made a CL.


Zettlr Markdown Editor

This PR adds the markdown editor Zettlr into the applications-list.
Project URL
https://github.com/Zettlr/Zettlr
Category
markdown
Description
This PR adds the Zettlr Markdown editor into the applications.json
Why it should be included to Awesome macOS open source applications  (optional)
It has a nice integration with pandoc to create pdf documents with markdown. I personally wrote some assignments with this editor.
Checklist

[x] Edit applications.json instead of README.md.
[x] Only one project/change is in this pull request
[x] Screenshots(s) added if any
[x] Has a commit from less than 2 years ago
[x] Has a clear README in English

          1 Warning

:warning:
Please rebase to get rid of the merge commits in this Pull Request

  Generated by :no_entry_sign: Danger

@serhii-londar how can I squash the commits?

@hayribakici Thank you! 👍


[Openshift] Secrets webhook breaks default SCC on 1.15.2

Describe the bug:
On Openshift, after upgrading from 1.15.1 to 1.15.2, the injector stops working correctly because initContainers are rejected by default security context constraint  ("restricted").
Steps to reproduce the bug:
Run the webhook 1.15.2 on Openshift 4.X
Why
This is introduced by :
https://github.com/banzaicloud/bank-vaults/pull/1562
https://github.com/banzaicloud/bank-vaults/commit/bd4da3a0397033c2a908ac02897a230812a489d2#diff-32802053da07acef355a6beb95cc5c4494d6d9c77ee709fb9093c7febb4bfc05L51
The init container is now rejected because :

It runs with user "0" even with vault.security.banzaicloud.io/run-as-non-root: "true"  - which is not tolerated by Openshift default "restricted" SCC
You cannot explicitely add any capability with Openshift default "restricted" SCC

Not sure what the solution is :

Would it be possible to add an annotation that removes completely the security context from the specs?  (would make sense in an Openshift environment, providing secure defaults)
If so, would the Openshift default capabilities be compatible with the secret webhook requirements? (reminder: it works fine with 1.15.1)
If not...  this is kinda of problem, because that would require to use a custom SCC for each project consuming secrets. Not really an option.

Thanks,
/kind bug

FYI I'm looking at this issue right now. I'll post an update as soon as I have a solution.

Hey folks!
I wanted to provide an update since I made some progress on this issue.
There are actually multiple problems and I haven't uncovered them all (also, I'm having difficulties with running tests on Openshift, but I'm getting there), but there are some issues that are clear at this point:
Firstly, I believe there is some misunderstanding about what the vault.security.banzaicloud.io/run-as-non-root annotation does. If you look into the Dockerfile you will see that it already runs as a non-root user normally. The annotation only sets runAsNonRoot in the security context.
Secondly (and this is why the containers running these security contexts actually ended up as running root), there is a bug in the current security context implementation. There is a second optional annotation called vault.security.banzaicloud.io/run-as-user. When the annotation is not set, its value falls back to 0 (due to how default values work in Go). Due to a bug, in the code runAsUser is set at the moment even when the annotation is not provided, setting the UID...you guessed it right, 0. That combined with vault.security.banzaicloud.io/run-as-non-root=true you get the error that all of you experienced.
Fortunately, this is an easy fix.
Another problem related to the security context is the default set of capabilities introduced in bank-vaults/bank-vaults#1562. Although I still have to verify this, but the PR says those capabilities are necessary for Vault Agent templating only. If that is the case, they can probably be removed from the default list of capabilities and added to a vault agent template specific init container.
I'm hoping to provide a PR in the next couple days.
The challenge is testing though to make sure the changes do not introduce any new regressions and that they actually solve the problem. If anyone wants to volunteer and help with testing, that would be great.


Allow ? in identifier names?

Predicates might benefit from allowing ? in, or maybe only at the end of, identifier names.
Stylistically, I'm not too sure about it - is-zero is a good alternative for zero?, and we use symbols nowhere else ( except for ' in .. names ).
Implementation is not hard, that would not be a reason not to do it.

closed by #106


Running a second instance of Gitea on the same storage path hangs

Gitea version (or commit ref): 1.6.4
Git version: 2.15.3
Operating system: Docker Image of Alpine 3.7
Database (use [x]):

[x] PostgreSQL
[ ] MySQL
[ ] MSSQL
[ ] SQLite

Can you reproduce the bug at https://try.gitea.io:

[ ] Yes (provide example URL)
[ ] No
[x] Not relevant

Log gist: N/A

Description
Running a second instance of Gitea using the same storage path hangs on startup on locking issues.bleve. This probably didn't happen to us on 1.5 due to the issue fixed by https://github.com/go-gitea/gitea/pull/5563.
Stack trace
 0  0x000000000043c4a9 in runtime.gopark
    at .usr/local/go/src/runtime/proc.go:292
 1  0x000000000043c55e in runtime.goparkunlock
    at .usr/local/go/src/runtime/proc.go:297
 2  0x000000000045a6db in time.Sleep
    at .usr/local/go/src/runtime/time.go:102
 3  0x0000000000dbb9b1 in code.gitea.io/gitea/vendor/github.com/boltdb/bolt.flock
    at .go/src/code.gitea.io/gitea/vendor/github.com/boltdb/bolt/bolt_unix.go:38
 4  0x0000000000dc4891 in code.gitea.io/gitea/vendor/github.com/boltdb/bolt.Open
    at .go/src/code.gitea.io/gitea/vendor/github.com/boltdb/bolt/db.go:186
 5  0x0000000000df8e2e in code.gitea.io/gitea/vendor/github.com/blevesearch/bleve/index/store/boltdb.New
    at .go/src/code.gitea.io/gitea/vendor/github.com/blevesearch/bleve/index/store/boltdb/store.go:77
 6  0x0000000000cd8911 in code.gitea.io/gitea/vendor/github.com/blevesearch/bleve/index/upsidedown.(*UpsideDownCouch).Open
    at .go/src/code.gitea.io/gitea/vendor/github.com/blevesearch/bleve/index/upsidedown/upsidedown.go:308
 7  0x0000000000e691a5 in code.gitea.io/gitea/vendor/github.com/blevesearch/bleve.openIndexUsing
    at .go/src/code.gitea.io/gitea/vendor/github.com/blevesearch/bleve/index_impl.go:168
 8  0x0000000000e67bd9 in code.gitea.io/gitea/vendor/github.com/blevesearch/bleve.Open
    at .go/src/code.gitea.io/gitea/vendor/github.com/blevesearch/bleve/index.go:248
 9  0x0000000000e90503 in code.gitea.io/gitea/modules/indexer.openIndexer
    at .go/src/code.gitea.io/gitea/modules/indexer/indexer.go:84
10  0x0000000000e90815 in code.gitea.io/gitea/modules/indexer.InitIssueIndexer
    at .go/src/code.gitea.io/gitea/modules/indexer/issue.go:55
11  0x00000000011b0211 in code.gitea.io/gitea/models.InitIssueIndexer
    at .go/src/code.gitea.io/gitea/models/issue_indexer.go:21
12  0x00000000014d03ff in code.gitea.io/gitea/routers.GlobalInit
    at .go/src/code.gitea.io/gitea/routers/init.go:72
13  0x0000000001805186 in code.gitea.io/gitea/cmd.runWeb
    at .go/src/code.gitea.io/gitea/cmd/web.go:121
14  0x00000000012f986e in code.gitea.io/gitea/vendor/github.com/urfave/cli.HandleAction
    at .go/src/code.gitea.io/gitea/vendor/github.com/urfave/cli/app.go:471
15  0x00000000012fb0e8 in code.gitea.io/gitea/vendor/github.com/urfave/cli.Command.Run
    at .go/src/code.gitea.io/gitea/vendor/github.com/urfave/cli/command.go:191
16  0x00000000012f7427 in code.gitea.io/gitea/vendor/github.com/urfave/cli.(*App).Run
    at .go/src/code.gitea.io/gitea/vendor/github.com/urfave/cli/app.go:241
17  0x000000000181804f in main.main
    at .go/src/code.gitea.io/gitea/main.go:53
18  0x000000000043c070 in runtime.main
    at .usr/local/go/src/runtime/proc.go:198
19  0x000000000046c081 in runtime.goexit
    at .usr/local/go/src/runtime/asm_amd64.s:2361

cc @zvikagart

I will test it.

We're working on deploying a multi-master Gitea using CephFS as shared storage for both git repos and blevesearch indexes.  We seemed to have the system working on 1.6.0, but suspect that we're hitting this issue after upgrading to 1.7.1.  The system is not in production yet, and we don't have much in the way of historical data to contribute to this bug report.  But if you do come up with a solution to this, we would be happy to help out with some fairly high-volume testing.

@jeblair any logs could you give?

I ran strace on the second gitea process I started and came to the same conclusion as @segevfiner, when I saw an open file handle to issues.bleve and flock syscalls.  Other than that, I didn't see much of use.  Is there anything I should look for?

Looking at the indexer code, it seems to be a nice clean interface (yay for interfaces!) What would people think about adding something like an optional elasticsearch driver that people trying to do larger installations could use, but keep the bleve implementation in as the default so that people don't have to install elasticsearch just to get a gitea?

@emonty that's exactly the plan :wink:

@techknowlogick sweet! that sounds like an excellent plan. 👍

@emonty https://github.com/go-gitea/gitea/pull/5363 just merged yesterday. The issues Indexer interface has been there and it's simple enough that somebody could send a PR to implement elasticsearch. And I will send a PR to refactor code search indexer similar with issue indexer.

I have sent https://github.com/go-gitea/gitea/pull/6144, then if you change ISSUE_INDEXER_TYPE to db will resolve the problem when you have a small deployment. And I will send another PR to add elasticsearch and redis.


Merge 1.6.14

Codecov Report

Merging #748 into master will increase coverage by 0.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #748      +/-   ##
==========================================
+ Coverage   68.39%   68.41%   +0.01%
==========================================
  Files         392      392
  Lines       20936    20944       +8
==========================================
+ Hits        14320    14329       +9
+ Misses       6616     6615       -1

Impacted Files
Coverage Δ

cask/lib/hbc/system_command.rb
99.07% <0%> (+0.01%)
:arrow_up:

cask/lib/hbc/artifact/installer.rb
85.71% <0%> (+4.31%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1cf32e4...87dea50. Read the comment docs.


Javascript conversion crashes during multipart form data

Hi,
In javascript code generation template you are doing deletion of content type header in case of multi part form data. Code crashes saying "Cannot read property 'indexOf' of undefined" if javascript conversion is called twice and if same snippet is converted to other language content header will be missing.
Ex:
var snippet = new HTTPSnippet(data);
console.log(snippet.convert('javascript'));
console.log(snippet.convert('javascript'));
Regards,
Karthik M L

can you provide an example?

Any post request with postdata having mimetype multipart formdata will do.


Cache files while restoring

Create tmp directory while restoring in order to cache files that have been moved.

The following requirements should be met during restoring:

Folders should not disappear during backup if they change just slightly.
Folders should not have an incomplete state over a long time during restoring.
The used disc space should not exceed the checkpoint size by large.
Duplicates should be handled correctly. Duhh


problem in viewing tooltip data in States - Growth Trend - Deep Dive

Describe the bug
The data available in the tooltip for States- Growth Trend (Deep-dive section) isn't visible distinctly. It is actually getting merge with a lot of background details. (a big problem for mobile users)
To Reproduce
Steps to reproduce the behavior:

Go to "Deep Dive"
Scroll down to "Growth trends graph"
Click on graph trend, and see the tooltip.

Expected behavior
Data should be clearly visible, because if anyone wants to take an insight on a point in the growth trend, then tooltip is the main source of it.
Screenshots
Attaching SS from 2 different devices:

Desktop (please complete the following information):

OS: macOS
Browser: Chrome
Version: 80.1

Smartphone (please complete the following information):

Device: Note 8, iphone7
OS: Android, iOS
Browser: Chrome
Version: 80.1

@jeremyphilemon @JunaidBabu
I am already fixing this, will send a PR soon.

@jeremyphilemon
I've already added a PR for this. I think this addition will solve the tooltip for growth trends and will make the overall experience better (I've also added the tooltip change for patients by nationality).
Hope you'll take a look at it soon.


Cluster monitoring operator changes for OCP 4.3

This commit:

Adds support to disable cluster-monitoring-operator
from being controlled by cvo to be able to run the monitoring
components on dedicated infra nodes.
Changes the default storage class to managed_premium as that's the
default storage class avaiable for OCP 4.3 installs.

Fixes https://github.com/openshift-scale/scale-ci-deploy/issues/47.

LGTM - Would of preferred two different PRs. One to address #47 and one to fix the storage class.. However, NBD.

Thanks for the review @jtaleric and @mohit-sheth.


Prevent onboarding process from being executed multiple times

Currently we do not check if a user already has setup an account or a password when accessing the welcome page.
To prevent a user from inconsistent config data (e.g. by setting different passwords) we should prevent accessing the welcome page if a user is already onboarded.

I could give this a try, could you point me to where the data is stored for if a user has already been onboarded? Is there a boolean value somewhere?

we have this status action: https://github.com/getAlby/lightning-browser-extension/blob/master/src/extension/background-script/actions/setup/status.js
that can be used like it is here: https://github.com/getAlby/lightning-browser-extension/blob/00c03bf895a295b90813de1b68d73f05959ea4f0/src/app/context/AuthContext.tsx#L31-L42
so if the status is completed we should redirect the user to the option page.

Sounds like we are still waiting on some details from #375 before continuing on this?

seems they are a bit independent. here we should only check that we redirect to the options page if an account is already setup (if setup is configured)

@bumi @secondl1ght
I grabbed this as my first issue, since it's quite an easy one. Hope that's okay. One thing that I was wondering is whether people used re-doing the onboarding process as a way to change their node for example. I guess that wouldn't be possible anymore with the redirect.

thanks!
users can change accounts from the options.
They must not go through the onboarding again, because that would could change the password and thus decrypting account data would fail.


Training fails

/usr/local/lib/python3.9/dist-packages/flax/core/frozen_dict.py:169: FutureWarning: jax.tree_util.register_keypaths is deprecated, and will be removed in a future release. Please use register_pytree_with_keys() instead.
jax.tree_util.register_keypaths(
'########:'########:::::'###::::'####:'##::: ##:'####:'##::: ##::'######:::
... ##..:: ##.... ##:::'## ##:::. ##:: ###:: ##:. ##:: ###:: ##:'##... ##::
::: ##:::: ##:::: ##::'##:. ##::: ##:: ####: ##:: ##:: ####: ##: ##:::..:::
::: ##:::: ########::'##:::. ##:: ##:: ## ## ##:: ##:: ## ## ##: ##::'####:
::: ##:::: ##.. ##::: #########:: ##:: ##. ####:: ##:: ##. ####: ##::: ##::
::: ##:::: ##::. ##:: ##.... ##:: ##:: ##:. ###:: ##:: ##:. ###: ##::: ##::
::: ##:::: ##:::. ##: ##:::: ##:'####: ##::. ##:'####: ##::. ##:. ######:::
:::..:::::..:::::..::..:::::..::....::..::::..::....::..::::..:::......::::
0% 0/1500 [00:00<?, ?it/s] Musti  Musti Traceback (most recent call last):
File "/content/diffusers/examples/dreambooth/train_dreambooth.py", line 803, in
main()
File "/content/diffusers/examples/dreambooth/train_dreambooth.py", line 668, in main
latents = vae.encode(batch["pixel_values"].to(dtype=weight_dtype)).latent_dist.sample()
File "/usr/local/lib/python3.9/dist-packages/diffusers/models/autoencoder_kl.py", line 158, in encode
h = self.encoder(x)
File "/usr/local/lib/python3.9/dist-packages/torch/nn/modules/module.py", line 1194, in _call_impl
return forward_call(*input, **kwargs)
File "/usr/local/lib/python3.9/dist-packages/diffusers/models/vae.py", line 105, in forward
sample = down_block(sample)
File "/usr/local/lib/python3.9/dist-packages/torch/nn/modules/module.py", line 1194, in _call_impl
return forward_call(*input, **kwargs)
File "/usr/local/lib/python3.9/dist-packages/diffusers/models/unet_2d_blocks.py", line 984, in forward
hidden_states = resnet(hidden_states, temb=None)
File "/usr/local/lib/python3.9/dist-packages/torch/nn/modules/module.py", line 1194, in _call_impl
return forward_call(*input, **kwargs)
File "/usr/local/lib/python3.9/dist-packages/diffusers/models/resnet.py", line 540, in forward
hidden_states = self.norm1(hidden_states)
File "/usr/local/lib/python3.9/dist-packages/torch/nn/modules/module.py", line 1194, in _call_impl
return forward_call(*input, **kwargs)
File "/usr/local/lib/python3.9/dist-packages/torch/nn/modules/normalization.py", line 273, in forward
return F.group_norm(
File "/usr/local/lib/python3.9/dist-packages/torch/nn/functional.py", line 2528, in group_norm
return torch.group_norm(input, num_groups, weight, bias, eps, torch.backends.cudnn.enabled)
torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 4.83 GiB (GPU 0; 14.75 GiB total capacity; 9.21 GiB already allocated; 4.47 GiB free; 9.25 GiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF
0% 0/1500 [00:04<?, ?it/s]
Traceback (most recent call last):
File "/usr/local/bin/accelerate", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.9/dist-packages/accelerate/commands/accelerate_cli.py", line 43, in main
args.func(args)
File "/usr/local/lib/python3.9/dist-packages/accelerate/commands/launch.py", line 837, in launch_command
simple_launcher(args)
File "/usr/local/lib/python3.9/dist-packages/accelerate/commands/launch.py", line 354, in simple_launcher
raise subprocess.CalledProcessError(returncode=process.returncode, cmd=cmd)
subprocess.CalledProcessError: Command '['/usr/bin/python3', '/content/diffusers/examples/dreambooth/train_dreambooth.py', '--image_captions_filename', '--train_only_unet', '--save_starting_step=500', '--save_n_steps=0', '--Session_dir=/content/gdrive/MyDrive/Fast-Dreambooth/Sessions/Musti', '--pretrained_model_name_or_path=/content/stable-diffusion-v2-768', '--instance_data_dir=/content/gdrive/MyDrive/Fast-Dreambooth/Sessions/Musti/instance_images', '--output_dir=/content/models/Musti', '--captions_dir=/content/gdrive/MyDrive/Fast-Dreambooth/Sessions/Musti/captions', '--instance_prompt=', '--seed=2339', '--resolution=512', '--mixed_precision=fp16', '--train_batch_size=1', '--gradient_accumulation_steps=1', '--use_8bit_adam', '--learning_rate=2e-06', '--lr_scheduler=linear', '--lr_warmup_steps=0', '--max_train_steps=1500']' returned non-zero exit status 1.
Something went wrong

are you using the latest notebook ?

are you using the latest notebook ?

yes i am

tested with different google accounts but always same issue

you're using the v-768 with 512 resolution ?

you're using the v-768 with 512 resolution ?

v-768

you're not using the latest notebook, use this https://colab.research.google.com/github/TheLastBen/fast-stable-diffusion/blob/main/fast-DreamBooth.ipynb

you're not using the latest notebook, use this https://colab.research.google.com/github/TheLastBen/fast-stable-diffusion/blob/main/fast-DreamBooth.ipynb

okay i will try <3

you're not using the latest notebook, use this https://colab.research.google.com/github/TheLastBen/fast-stable-diffusion/blob/main/fast-DreamBooth.ipynb

Trainng went good now but when im gonna test it this comes up
Traceback (most recent call last):
File "/content/gdrive/MyDrive/sd/stable-diffusion-webui/webui.py", line 25, in
import gradio
File "/usr/local/lib/python3.9/dist-packages/gradio/init.py", line 3, in
import gradio.components as components
File "/usr/local/lib/python3.9/dist-packages/gradio/components.py", line 35, in
from gradio.blocks import Block, BlockContext
File "/usr/local/lib/python3.9/dist-packages/gradio/blocks.py", line 27, in
from gradio.helpers import EventData, create_tracker, skip, special_args
ImportError: cannot import name 'EventData' from 'gradio.helpers' (/usr/local/lib/python3.9/dist-packages/gradio/helpers.py)

I'm getting the same CUDA error training using the Dreamshaper model from Hugginface (1.5, 512). It was all well last week.
PS: I checked and I do use the latest notebook.


Fix the errors of the console window for Register/Login Modal

User Story:
I want to debug the Register/Login Modal's console,
So that we can see the changes in the console window without errors.

Acceptance Criteria:

[x] Console window is without errors.

We are not using this issue.


Do we need some specific version of torch.

Hello,
I am trying to install the software on MAC-M1 and I get the following error. Is there any specific version of torch required for this software?
File "/private/var/folders/kb/dq9v0bpn67gb64fkjtrvs38c0000gn/T/pip-build-env-bjc87d02/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
self.run_setup()
File "/private/var/folders/kb/dq9v0bpn67gb64fkjtrvs38c0000gn/T/pip-build-env-bjc87d02/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 507, in run_setup
super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
File "/private/var/folders/kb/dq9v0bpn67gb64fkjtrvs38c0000gn/T/pip-build-env-bjc87d02/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
exec(code, locals())
File "", line 27, in
ModuleNotFoundError: No module named 'torch'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build editable did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.

I realized that without calling pip install -e . the code works.

The setup.py file imports torch before resolving the requirements.txt file to get some version information I think.
I solved this by installing torch before running pip install -e .


Add discrete algorithm

Pull Request Test Coverage Report for Build 416289019

51 of 52 (98.08%)  changed or added relevant lines in 3 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.4%) to 97.59%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/discrete.jl
25
26
96.15%

Totals

Change from base Build 415707413:
-0.4%

Covered Lines:
81

Relevant Lines:
83

💛  - Coveralls


lower tls_inspector initial_read_buffer_size

Describe the feature request
We've been hit by the same issue as reported in envoy: https://github.com/envoyproxy/envoy/issues/34706
As stated in this comment tls_inspector default initial_read_buffer_size is 64kb which is a lot and causes a lot of memory to be used when there is a lot of active connections.
It would be great to find an ideal standard size to set for Istio deployments, and probably be able to tune this for different listeners, for example:

ingress listeners receive mtls client hello from other sidecars, we could check what's the standard size of those packets.
egress listeners i think usually don't receive much tls traffic a much less frequently mtls traffic, we could further reduce the size read from these listeners.

Tweaking this configuration is pretty safe because if the filter needs more data, then it continues double the read buffer size until 64kb is reached which is the maximum. So in the worst case scenario we would end up performing more socket reads, which shouldn't be too bad.
To take into consideration, http_inspector reads only 8k which is 8 times less.
Describe alternatives you've considered
Affected product area (please put an X in all that apply)
[ ] Ambient
[ ] Docs
[ ] Dual Stack
[ ] Installation
[x] Networking
[x] Performance and Scalability
[ ] Extensions and Telemetry
[ ] Security
[ ] Test and Release
[ ] User Experience
[ ] Developer Infrastructure
Affected features (please put an X in all that apply)
[ ] Multi Cluster
[ ] Virtual Machine
[ ] Multi Control Plane
Additional context

I agree. While TLS RFCs do not limit the size of a client hello, 64k is pretty high.  TLS Max record size it self is 16k I think. We can safely reduce it to 8k atleast.


One of the environment variable is missing from .env.example

ENABLE_SEARCH_OPENROUTER="" is missing and SEARCH_API="" can't be empty even after setting ENABLE_SEARCH_OPENROUTER="false"

@Abdalnablse10 Should be fixed in #262


terminal.integrated.defaultProfile and terminal.integrated.automationProfile behaves differently

Does this issue occur when all extensions are disabled?: Yes

VS Code Version: 1.64.0-insider (user setup)
OS Version: Windows_NT x64 10.0.19044

I can define my preferred terminal profile using the terminal.integrated.profiles.linux setting:
    "terminal.integrated.profiles.linux": {
        "zsh": {
            "path": "zsh",
            "args": [
                "--login"
            ],
            "env": {
                "TMUX": "false"
            }
        }
    },

...and I can specify this profile (referring to it by name) as my defaultProfile:
    "terminal.integrated.defaultProfile.linux": "zsh",

So this works fine for the standard built-in Terminal in VS Code.
However, I also want to use this terminal profile in the debugging-terminals. And according to the documentation, the setting terminal.integrated.automationProfile.linux should work like the terminal.integrated.defaultProfile.linux, allowing me to specify:
    "terminal.integrated.automationProfile.linux": "zsh",

But this does NOT work. The setting terminal.integrated.automationProfile.linux expects a dictionary/object like the terminal.integrated.profiles setting. But it only accepts keywords path and icon, so I'm not able to specify the args and env that I need.
Proposed fix: Make sure terminal.integrated.automationProfile behaves like terminal.integrated.defaultProfile (and according to the documentation), allowing us to specify a profile name defined in the terminal.integrated.profiles setting.

Passing over to @alexr00, not sure how tightly you want to control the environment/args in the automation profile. I'm guessing changing args isn't possible right now.

I have the same problem (on Windows 10 using Visual Studio Code 1.66.0) and in my opinion it is more of a bug than a feature request.
Based on the naming and description I would expect terminal.integrated.automationProfile to behave the same as the terminal.integrated.defaultProfile setting (that is, it should be set to a profile name defined under terminal.integrated.profiles). But I cannot even provide a dictionary/object to it, because when I try to do so, I receive the following message from Visual Studio Code: Incorrect type. Expected "null".
So it just seems to be impossible to use the terminal.integrated.automationProfile at all.

Is there any movement on this issue?
I am trying to debug using the terminal and I cannot set my node.js version because of this issue.
There is not good documentation / intellisense, or examples as to why this breaks or how to configure your debug terminal vs the integrated terminal. Everything piece of documentation I have found isn't very clear on how to do this.
The VsCode documentation seems to be out of date with respect to this updated configuration.
TL;DR - I can't figure out how to configure the JS debug terminal to run the proper version of Node.js that works fine in my integrated terminal.

@ontoneio this issue is specific to tasks/debug, the JS debug terminal is different and actually part of the js-debug extension: https://github.com/microsoft/vscode-js-debug

Similar same problem here. I need to configure the env variables for automation profile to use with attach debugger.
The automation profile only works for tasks with the setting:
"type": "shell"

When launch the debugger, the automation profile env do not work at all.

What is the state of this issue ?
Solving this provides a solution to https://code.visualstudio.com/docs/editor/tasks#_why-do-i-get-command-not-found-when-running-a-task. Currently nvm or sdkman are unusable with vscode. This makes it very hard to work on multiple projects with different tools (node/npm but also java/maven/grddle).


xboxswap not working

Version
20220909
Describe the bug
The "xboxswap" command does not work despite having theoretically done the swap procedure correctly.
Screenshots
DiscImageCreator.exe xboxswap G X:\mgs2.iso 16<PHONE_NUMBER>08<PHONE_NUMBER>18 1066092 1218024 1377954 1527140 2218604 2367520 2526692 2681858 2832350 2991436 3143584 3453874
Disc title
Metal Gear Solid 2: Substance
Disc ringcode
Unknown
URL
Tell me the link to get the disc.
Amazon: https://www.amazon.com/Metal-Gear-Solid-2-Substance-xbox/dp/B00006F2ZQ/ref=sr_1_5?keywords=metal+gear+solid+xbox&qid=1669684247&sr=8-5
eBay: https://www.ebay.com/sch/i.html?_from=R40&_trksid=m570.l1313&_nkw=metal+gear+solid+2+xbox&_sacat=0
discogs:
Log file
stranger_20220809T091705.txt
stranger_disc.txt
stranger_drive.txt
stranger_mainError.txt
stranger_mainInfo.txt
stranger_volDesc.txt
mgs2_20220909T220450.txt
mgs2_disc.txt
mgs2_drive.txt
mgs2_mainError.txt
mgs2_mainInfo.txt
mgs2_volDesc.txt
The drive I'm using is an iHAS124. If I run the command quickly after the drive closes, I get NOT_READY - LUN_NOT_READY - BECOMING_READY rather than the error from the log files. Similar results with test version. Is the problem with my drive, my trap disk, or something else?
EDIT: uploaded the wrong log files

mgs2_mainError.txt says

NOT_READY - MEDIUM NOT PRESENT - TRAY CLOSED

It seems the drive failed to recognize the trap disc.

That’s the error message I’m getting after swapping the game. It reads the trap disk just fine.

The size of the trap disc is short. Your disc is 3629408, but 3820880 is needed to use xboxswap.

I was able to get xboxswap to begin copying the game once I created an image file of the right length and an mds file that specified the right layerbreak, burned it to a DVD, then removed the drive cover instead of using the emergency eject method.
When I used the emergency eject method, I got the same results as initially. However, at precisely the layerbreak, I get the results shown in the following log files.
mgs2_20220909T220450.txt
mgs2_disc.txt
mgs2_drive.txt
mgs2_mainError.txt
mgs2_mainInfo.txt
mgs2_volDesc.txt
Since it's at the layerbreak, I suspect it may be an issue with how the trap disc was burned as defined by the mds file. Would using PTP or OTP be correct for an XBOX game, or is that even what the issue is?

Was dumping failed partway?

Yes. Dumping failed once it reach the layerbreak.

https://github.com/saramibreak/DiscImageCreator/wiki#how-to-create
XBOX: DVD (Length is 3820880 or larger, Layerbreak is 1913776 or larger)

Did you prepare the DVD that has above enough size to create the trap disc?
Setting LayerBreak manually (L0 sector num is about a half size of DVD length)
e.g. If DVD length is 3900304, L0 sector num is about 1950160

Did you set LayerBreak correctly?

According to ImgBurn, My image has 3820880 sectors and the layerbreak is set at 1913776.

I burned this image to a blank DVD+R DL.

The advice I can is here...

Try to dump other xbox disc. If it's success, the burned image is no problem.
If other xbox disc also fails to dump, please create the image file using length is larger than 3820880 and layerbreak is larger than 1913776.
If still it fails, change the other drive.

I have yet to successfully dump a disc, but I have done some further testing. Any other game on the iHAS124 has failed immediately with L-EC - UNCORRECTABLE ERROR. However, after switching drives, specifically to a Hitachi-LG GSA-H30L, it is now failing with MEDIUM_ERROR - ID CRC OR ECC ERROR, which is new. Also, with some of my games I've actually gotten a partial dump out of them. Here are some log files from all the ones from which I've gotten a partial dump:
stranger_disc.txt
stranger_drive.txt
stranger_mainError.txt
stranger_mainInfo.txt
stranger_volDesc.txt
kotor_disc.txt
kotor_drive.txt
kotor_mainError.txt
kotor_volDesc.txt
kotor_mainInfo.txt
mgs2_20220809T091705.txt
mgs2_disc.txt
mgs2_drive.txt
mgs2_mainError.txt
mgs2_mainInfo.txt
mgs2_volDesc.txt
With these results in mind, is the problem at this point that my game discs are just bad? None of them are in pristine condition, though the amount of damage varies. They do all still play on an actual xbox, however.

I only confirmed it by GSA-4163B. I'm not sure but your drive may not support...

I only confirmed it by GSA-4163B. I'm not sure but your drive may not support...


Blinking border #2

Ah I got excited for a moment but look :

Tbh maybe it's an issue on my end, completely possible.
You can see the  blinking border is " styled " now.
Reposting this here for clarity sake, remove if that's annoying.

Okay you know what, I must be crazy. I'm trying it right now again and it looks like it's working ?
Sorry about that and thanks for your work, I enjoy it :)


[vcpkg baseline][libqcow] Update to new version

Describe the pull request

What does your PR fix?
Update libqcow to new version and fix download source failed.

ping @dan-shaw for review and merge this PR, this blocked the pipeline test.

/azp run

/azp run

Thanks for your contribution!


Hide crates list from the ui

It would be very useful for me to be able to hide crates list and their metadata from the ui with a setting in the config if a user is not logged in

I've set registry.auth_required settings to true but still I can search crates being logged out. And I see their dependencies, documentation, etc

Nevermind. I've put config to the wrong directory so it hasn't been loaded


Navigation & Footer

Prerequisites

[X] I am an Open Source Contributor
[X] I checked to make sure that this issue has not already been filed

Description
I want to add a Footer and navigation section for this game under JWOC
Screenshots
No response
Code of Conduct

[X] I follow Contributing Guidelines of this project.

Pls specify what navigation you want to add?

This type of navigation i want to add in your web, please assign me

This type of footer i want to add, please assign me

Navigation is not needed since there are not many sections.
You can go for the footer and make it properly and responsive so that it should not affect the game @Keshab1113

Okey, assign me
On Sun, 19 Feb, 2023, 12:55 Rakesh Roshan, @.***> wrote:

Navigation is not needed since there are not many sections.
You can go for the footer and make it properly and responsive so that it
should not affect the game @Keshab1113 https://github.com/Keshab1113
—
Reply to this email directly, view it on GitHub
https://github.com/Rakesh9100/Click-The-Edible-Game/issues/46#issuecomment-1435914108,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/A2NHGP5BWVWFL6OMNDSDSMTWYHDIJANCNFSM6AAAAAAVAE7VWU
.
You are receiving this because you were mentioned.Message ID:
@.***>


BST: Reconstruct BST in C++

Reconstruct BST
	The pre-order traversal of a Binary Tree is a traversal technique that starts at the tree's root
        node and visits nodes in the following order:
		Current Node
		Left Subtree
		Right Subtree

  	Given a non-empty array of integers representing the pre-order traversal of a Binary Search Tree
        (BST), write a function that creates the relevant BST and returns its root node.

        The input array will contain the values of BST nodes in the order in which these nodes would be
        visited with a pre-order traversal.
	Sample Input: [10, 4, 2, 1, 5, 17, 19, 18]
	Sample Output:
	10
      /    \
     4      17
   /   \      \
  2     5     19
 /           /
1           18

I'll take this up

assign this to me @akgmage

#1276 and #1275
I have solved the problem here  and have attached relevant explanation to it too
Happy Learning !!!

I'll take this up @akgmage

I'll take this up


How to generate count matrix after generating output from kallisto pseudo

Can you guide me how to generate count matrix after generating output from kallisto pseudo --quant -i reference/index.idx -o ./mop_SMARTseq/out/ -b smart-seq_batch.txt -t 16 for downstream alalysis in SMART-SEQ2
I got this many files from Kallisto pseudo --quant
1, matrix.abundance.mtx
2, matrix.cells
3, matrix.ec
4, matrix.fld.tsv
5, matrix.tcc.mtx
6, run_info.json
7, transcripts.txt
Which file I should use for generating isoform count matrices file for downstream analysis. also i would like to know how did create "adata.h5ad" file?
Thanks
JKT

Hello JKT,
Could you manage to get count matrix?
Thank you.
Best
ASh

Please see this script: https://github.com/pachterlab/BYVSTZP_2020/blob/master/analysis/scripts/make_adata.py


BLS Exception Handling

This PR was merged manually.  See https://github.com/dashevo/dashj/commit/6a666c3e73278fe022f13cdd23a6620cebe7e4f5


oh-my-zsh git status for modular git section

Adds support for the oh-my-zsh-style Git status Spaceship used until v3 / #147. This takes care of #355, where established users don't see the Git status they've come to expect and rely on.
Relies on the modular Git section in PR #391. I picture merging 391 first and then merging in only the second commit in this PR (not completely sure if GitHub will be smart about adjusting that diff or if I'd have to close and open a fresh PR). So logistically a little messy, but I wanted to provide an example of 391's value
Changes: 5be1b89 / sections/git_status_oh_my_zsh.zsh (jump link)

Frozen till decision made on #391.

I believe this might be implemented as an external section. Please use this template: https://github.com/spaceship-prompt/spaceship-section


Documentation updates

Customer feedback and improvements in the documentation. Added some trouble shooting items.

@Nidhi251289 Reviewed. Waiting for the test build to run before merging. Let me know if there's anything you'd like me to correct.


go install fails

See:
$ go install github.com/bcicen/ctop@latest
go: downloading github.com/bcicen/ctop v0.7.6
go install: github.com/bcicen/ctop@latest (in github.com/bcicen/ctop@v0.7.6):
	The go.mod file for the module providing named packages contains one or
	more replace directives. It must not contain directives that would cause
	it to be interpreted differently than if it were the main module.

I notice there is a replace directive in the go.mod file. We should not do this. Perhaps let's upgrade the dependency or fix what issue it has upstream? Or fork it.

replace directive has been removed in https://github.com/bcicen/ctop/commit/6dcb62f172bbb042893f81c7004c1ab361724a63


Invoice number length should be number of zeros that appears before invoice id.

Bug report
Title
Invoice number length should be number of zeros that appears before invoice id.
Issue Description
Invoice number length should be number of zeros that appears before invoice id.Currently the length allows how long the invoice number should be.
Preconditions
1. framework Version- 0.1.6

Steps to reproduce
1. step1- Set the Invoice Number Length to 1.
2. step2- Place 10 orders and generate invoice.

Expected result
Invoice number length should be number of zeros that appears before invoice id.

Actual result
Not working accordingly if invoice number length is less than invoice

Framework Version: 0.1.6

Fixed


Suggest closely related parameter name when a given one is not found

Please describe the feature you'd like
We could check the wrong parameter and suggest one that closely matches it. This can be done using some implementation of the Levenshtein distance, there are some implementations available
Why is it relevant?
Given the huge number of parameters haddock has, if you input a wrong parameter, it might be tricky to figure out what is the correct name. For that you'll need to go back to the documentation/code and find out the correct name.
Additional context (if any)

@douweschulte implemented it in HADDOCK3 here.

indeed, best if it's handled directly there


How to output the crowd count ?

Hello, when I run test.py I get the grayscale density maps, however I don't find the crowd count like it is outputted in your paper. How do we get it ?

exactly how to get the crowd count??

I also want to know how can i use the saved_models to calculate the crowd count

I did it just print the gt_count() and et_count() that's it.If you want to save it write it into file at the last line in train.py


Spatial interpolation

Use 50 nearest neighbors by default in empirical line interpolation. Ameliorates occasional segmentation artifacts in high contrast areas.  Ideally someday we can make smaller  segments and include even more neighbors in the calculation.

Thanks David!  Looks like a perfectly reasonable interim solution.