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[ci skip] Merge PR 25392
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Merge PR #25392, commits were: 
 * remove create test data (as workaround)

for

```
Traceback (most recent call last):
  File "/home/circleci/project/miniconda/bin/bioconda-utils", line 8, in <module>
    sys.exit(main())
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 971, in main
    bioconductor_skeleton, clean_cran_skeleton, autobump, bot
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 328, in dispatch_commands
    dispatch(parser, *args, **kwargs)
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 174, in dispatch
    for line in lines:
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 277, in _execute_command
    for line in result:
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/argh/dispatching.py", line 260, in _call
    result = function(*positional, **keywords)
  File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 130, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 59, in wrapper
    func(*args, **kwargs)
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/cli.py", line 476, in build
    keep_old_work=keep_old_work)
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/build.py", line 343, in build_recipes
    linter=linter)
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/build.py", line 149, in build
    pkg_test.test_package(pkg_path, base_image=base_image)
  File "/home/circleci/project/miniconda/lib/python3.7/site-packages/bioconda_utils/pkg_test.py", line 170, in test_package
    p = utils.run(cmd, env=env, cwd=d, mask=False)
  File "/home/circleci/project/miniconda/lib/python3.7/tempfile.py", line 805, in __exit__
    self.cleanup()
  File "/home/circleci/project/miniconda/lib/python3.7/tempfile.py", line 809, in cleanup
    _shutil.rmtree(self.name)
  File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 485, in rmtree
    _rmtree_safe_fd(fd, path, onerror)
  File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 423, in _rmtree_safe_fd
    _rmtree_safe_fd(dirfd, fullname, onerror)
  File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 443, in _rmtree_safe_fd
    onerror(os.unlink, fullname, sys.exc_info())
  File "/home/circleci/project/miniconda/lib/python3.7/shutil.py", line 441, in _rmtree_safe_fd
    os.unlink(entry.name, dir_fd=topfd)
PermissionError: [Errno 13] Permission denied: 'Intervene_pairwise_frac_matrix.txt'
```
 * add proper tests to intervene

- remove/invert restriction on pandas which was fixed in 0.6.5 asntech/intervene#40 (comment)
- running the tool outputs deprection warnings for matplotlib >= 3.4 ..
so I added a version restriction
  • Loading branch information
bernt-matthias authored Nov 17, 2020
1 parent 5d94bba commit 4088aea
Showing 1 changed file with 8 additions and 3 deletions.
11 changes: 8 additions & 3 deletions recipes/intervene/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ source:

build:
noarch: python
number: 0
number: 1
rpaths:
- lib/R/lib/
- lib/
Expand All @@ -22,8 +22,8 @@ requirements:
- bedtools >=2.29.1
- pysam >=0.15
- pybedtools
- matplotlib-base
- pandas <1.0.0
- matplotlib-base <3.4
- pandas >=1.0.0
- numpy
- scipy
- seaborn
Expand All @@ -45,6 +45,11 @@ test:
- intervene.modules.venn
commands:
- intervene --help
- intervene pairwise --test
- intervene venn --test
- intervene upset --test
# workaround for bioconda testing can not remove (PermissionError) created test data
- rm -rf Intervene_results

about:
home: https://github.com/asntech/intervene
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