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LoadLibrary error when invoking conda-build on Windows #10211

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gwerbin opened this issue Oct 17, 2018 · 2 comments
Closed

LoadLibrary error when invoking conda-build on Windows #10211

gwerbin opened this issue Oct 17, 2018 · 2 comments

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@gwerbin
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gwerbin commented Oct 17, 2018

Originally filed at conda/conda-build#3220

This is unlikely anything to do with conda-build; probably some badly written software has installed some non-system DLLs in your C:\Windows\System32 folder. Please open an issue at https://github.com/anaconda-issues/issues

conda/conda-build#3220 (comment)

Actual Behavior

$ conda build
Traceback (most recent call last):
  File "C:\Anaconda3\Scripts\conda-build-script.py", line 6, in <module>
    from conda_build.cli.main_build import main
  File "C:\Anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 18, in <module>
    import conda_build.api as api
  File "C:\Anaconda3\lib\site-packages\conda_build\api.py", line 22, in <module>
    from conda_build.config import Config, get_or_merge_config, DEFAULT_PREFIX_LENGTH as _prefix_length
  File "C:\Anaconda3\lib\site-packages\conda_build\config.py", line 17, in <module>
    from .variants import get_default_variant
  File "C:\Anaconda3\lib\site-packages\conda_build\variants.py", line 15, in <module>
    from conda_build.utils import ensure_list, trim_empty_keys, get_logger
  File "C:\Anaconda3\lib\site-packages\conda_build\utils.py", line 10, in <module>
    import libarchive
  File "C:\Anaconda3\lib\site-packages\libarchive\__init__.py", line 1, in <module>
    from .entry import ArchiveEntry
  File "C:\Anaconda3\lib\site-packages\libarchive\entry.py", line 6, in <module>
    from . import ffi
  File "C:\Anaconda3\lib\site-packages\libarchive\ffi.py", line 27, in <module>
    libarchive = ctypes.cdll.LoadLibrary(libarchive_path)
  File "C:\Anaconda3\lib\ctypes\__init__.py", line 434, in LoadLibrary
    return self._dlltype(name)
  File "C:\Anaconda3\lib\ctypes\__init__.py", line 356, in __init__
    self._handle = _dlopen(self._name, mode)
TypeError: LoadLibrary() argument 1 must be str, not None

Expected Behavior

$ conda build
usage: conda-build [-h] [-V] [-n] [--output] [--python PYTHON] [--perl PERL]
                   [--numpy NUMPY] [--R R_BASE] [--lua LUA]
                   [--bootstrap BOOTSTRAP]
                   [--append-file APPEND_SECTIONS_FILE]
                   [--clobber-file CLOBBER_SECTIONS_FILE]
                   [-m VARIANT_CONFIG_FILES] [--old-build-string] [--check]
                   [--no-anaconda-upload] [--no-include-recipe] [-s] [-t]
                   [--no-test] [-b] [-p] [--skip-existing] [--keep-old-work]
                   [--dirty] [-q] [--debug] [--token TOKEN] [--user USER]
                   [--no-force-upload] [--password PASSWORD] [--sign SIGN]
                   [--sign-with SIGN_WITH] [--identity IDENTITY]
                   [--config-file CONFIG_FILE] [--repository REPOSITORY]
                   [--no-activate] [--no-build-id] [--croot CROOT] [--verify]
                   [--output-folder OUTPUT_FOLDER]
                   [--no-prefix-length-fallback] [--prefix-length-fallback]
                   [--prefix-length _PREFIX_LENGTH] [--no-locking]
                   [--no-remove-work-dir] [--long-test-prefix]
                   [--no-long-test-prefix] [--keep-going]
                   [--cache-dir CACHE_DIR] [--no-copy-test-source-files]
                   [-c CHANNEL] [--override-channels]
                   RECIPE_PATH [RECIPE_PATH ...]
conda-build: error: the following arguments are required: RECIPE_PATH

Steps to Reproduce

Not sure.

I ran

conda upgrade -n base conda-build conda-env conda-verify conda-execute

which might have been a bad idea.

I had also recently uninstalled Visual Studio and reinstalled the Visual Studio build tools for both 2015 and 2017. I can probably just reinstall Anaconda at this point, but I want to make sure it's not a bug with Conda/Conda-build/Anaconda.

Anaconda or Miniconda version:

Anaconda 5.3.0

Operating System:

Windows 7 Enterprise SP 1

conda info
     active environment : None
       user config file : C:\Users\<redacted>\.condarc
 populated config files : C:\Users\<redacted>\.condarc
          conda version : 4.5.11
    conda-build version : 3.16.1
         python version : 3.7.0.final.0
       base environment : C:\Anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/win-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/win-64
                          https://repo.anaconda.com/pkgs/pro/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
                          https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : C:\Anaconda3\pkgs
                          C:\Users\<redacted>\AppData\Local\conda\conda\pkgs
       envs directories : C:\Anaconda3\envs
                          C:\Users\<redacted>\AppData\Local\conda\conda\envs
                          C:\Users\<redacted>\.conda\envs
               platform : win-64
             user-agent : conda/4.5.11 requests/2.19.1 CPython/3.7.0 Windows/7 Windows/6.1.7601
          administrator : True
             netrc file : None
           offline mode : False
conda list --show-channel-urls
$ conda list --show-channel-urls -n base
# packages in environment at C:\Anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0    defaults
alabaster                 0.7.11                   py37_0    defaults
anaconda                  5.3.0                    py37_0    defaults
anaconda-client           1.7.2                    py37_0    defaults
anaconda-navigator        1.9.2                    py37_0    defaults
anaconda-project          0.8.2                    py37_0    defaults
appdirs                   1.4.3            py37h28b3542_0    defaults
asn1crypto                0.24.0                   py37_0    defaults
astroid                   2.0.4                    py37_0    defaults
astropy                   3.0.4            py37hfa6e2cd_0    defaults
atomicwrites              1.2.1                    py37_0    defaults
attrs                     18.2.0           py37h28b3542_0    defaults
automat                   0.7.0                    py37_0    defaults
babel                     2.6.0                    py37_0    defaults
backcall                  0.1.0                    py37_0    defaults
backports                 1.0                      py37_1    defaults
backports.shutil_get_terminal_size 1.0.0                    py37_2    defaults
beautifulsoup4            4.6.3                    py37_0    defaults
bitarray                  0.8.3            py37hfa6e2cd_0    defaults
bkcharts                  0.2                      py37_0    defaults
blas                      1.0                         mkl    defaults
blaze                     0.11.3                   py37_0    defaults
bleach                    2.1.4                    py37_0    defaults
blosc                     1.14.4               he51fdeb_0    defaults
bokeh                     0.13.0                   py37_0    defaults
boto                      2.49.0                   py37_0    defaults
bottleneck                1.2.1            py37h452e1ab_1    defaults
bzip2                     1.0.6                hfa6e2cd_5    defaults
ca-certificates           2018.03.07                    0    defaults
cachecontrol              0.12.5                   py37_0    defaults
certifi                   2018.8.24                py37_1    defaults
cffi                      1.11.5           py37h74b6da3_1    defaults
chardet                   3.0.4                    py37_1    defaults
click                     6.7                      py37_0    defaults
cloudpickle               0.5.5                    py37_0    defaults
clyent                    1.2.2                    py37_1    defaults
colorama                  0.3.9                    py37_0    defaults
comtypes                  1.1.7                    py37_0    defaults
conda                     4.5.11                   py37_0    defaults
conda-build               3.16.1                   py37_0    defaults
conda-env                 2.6.0                         1    defaults
conda-execute             0.9.0                      py_0    conda-forge
conda-verify              3.1.1                    py37_0    defaults
console_shortcut          0.1.1                         3    defaults
constantly                15.1.0           py37h28b3542_0    defaults
contextlib2               0.5.5                    py37_0    defaults
cryptography              2.3.1            py37h74b6da3_0    defaults
curl                      7.61.0               h7602738_0    defaults
cycler                    0.10.0                   py37_0    defaults
cython                    0.28.5           py37h6538335_0    defaults
cytoolz                   0.9.0.1          py37hfa6e2cd_1    defaults
dask                      0.19.1                   py37_0    defaults
dask-core                 0.19.1                   py37_0    defaults
datashape                 0.5.4                    py37_1    defaults
decorator                 4.3.0                    py37_0    defaults
defusedxml                0.5.0                    py37_1    defaults
distributed               1.23.1                   py37_0    defaults
docutils                  0.14                     py37_0    defaults
entrypoints               0.2.3                    py37_2    defaults
et_xmlfile                1.0.1                    py37_0    defaults
fastcache                 1.0.2            py37hfa6e2cd_2    defaults
filelock                  3.0.8                    py37_0    defaults
flask                     1.0.2                    py37_1    defaults
flask-cors                3.0.6                    py37_0    defaults
freetype                  2.9.1                ha9979f8_1    defaults
future                    0.16.0                   py37_0    defaults
get_terminal_size         1.0.0                h38e98db_0    defaults
gevent                    1.3.6            py37hfa6e2cd_0    defaults
glob2                     0.6                      py37_0    defaults
greenlet                  0.4.15           py37hfa6e2cd_0    defaults
h5py                      2.8.0            py37h3bdd7fb_2    defaults
hdf5                      1.10.2               hac2f561_1    defaults
heapdict                  1.0.0                    py37_2    defaults
html5lib                  1.0.1                    py37_0    defaults
hyperlink                 18.0.0                   py37_0    defaults
icc_rt                    2017.0.4             h97af966_0    defaults
icu                       58.2                 ha66f8fd_1    defaults
idna                      2.7                      py37_0    defaults
imageio                   2.4.1                    py37_0    defaults
imagesize                 1.1.0                    py37_0    defaults
incremental               17.5.0                   py37_0    defaults
intel-openmp              2019.0                      118    defaults
ipykernel                 4.10.0                   py37_0    defaults
ipython                   6.5.0                    py37_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
ipywidgets                7.4.1                    py37_0    defaults
isort                     4.3.4                    py37_0    defaults
itsdangerous              0.24                     py37_1    defaults
jdcal                     1.4                      py37_0    defaults
jedi                      0.12.1                   py37_0    defaults
jinja2                    2.10                     py37_0    defaults
jpeg                      9b                   hb83a4c4_2    defaults
jsonschema                2.6.0                    py37_0    defaults
jupyter                   1.0.0                    py37_7    defaults
jupyter_client            5.2.3                    py37_0    defaults
jupyter_console           5.2.0                    py37_1    defaults
jupyter_core              4.4.0                    py37_0    defaults
jupyterlab                0.34.9                   py37_0    defaults
jupyterlab_launcher       0.13.1                   py37_0    defaults
keyring                   13.2.1                   py37_0    defaults
kiwisolver                1.0.1            py37h6538335_0    defaults
lazy-object-proxy         1.3.1            py37hfa6e2cd_2    defaults
libarchive                3.3.3                h798a506_0    defaults
libcurl                   7.61.0               h7602738_0    defaults
libiconv                  1.15                 h1df5818_7    defaults
libpng                    1.6.34               h79bbb47_0    defaults
libsodium                 1.0.16               h9d3ae62_0    defaults
libssh2                   1.8.0                hd619d38_4    defaults
libtiff                   4.0.9                h36446d0_2    defaults
libxml2                   2.9.8                hadb2253_1    defaults
libxslt                   1.1.32               hf6f1972_0    defaults
llvmlite                  0.24.0           py37h6538335_0    defaults
locket                    0.2.0                    py37_1    defaults
lockfile                  0.12.2                   py37_0    defaults
lxml                      4.2.5            py37hef2cd61_0    defaults
lz4-c                     1.8.1.2              h2fa13f4_0    defaults
lzo                       2.10                 h6df0209_2    defaults
m2w64-gcc-libgfortran     5.3.0                         6    defaults
m2w64-gcc-libs            5.3.0                         7    defaults
m2w64-gcc-libs-core       5.3.0                         7    defaults
m2w64-gmp                 6.1.0                         2    defaults
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    defaults
markupsafe                1.0              py37hfa6e2cd_1    defaults
matplotlib                2.2.3            py37hd159220_0    defaults
mccabe                    0.6.1                    py37_1    defaults
menuinst                  1.4.14           py37hfa6e2cd_0    defaults
mistune                   0.8.3            py37hfa6e2cd_1    defaults
mkl                       2019.0                      118    defaults
mkl-service               1.1.2            py37hb217b18_5    defaults
mkl_fft                   1.0.4            py37h1e22a9b_1    defaults
mkl_random                1.0.1            py37h77b88f5_1    defaults
more-itertools            4.3.0                    py37_0    defaults
mpmath                    1.0.0                    py37_2    defaults
msgpack-python            0.5.6            py37he980bc4_1    defaults
msys2-conda-epoch         20160418                      1    defaults
multipledispatch          0.6.0                    py37_0    defaults
navigator-updater         0.2.1                    py37_0    defaults
nbconvert                 5.4.0                    py37_1    defaults
nbformat                  4.4.0                    py37_0    defaults
networkx                  2.1                      py37_0    defaults
nltk                      3.3.0                    py37_0    defaults
nose                      1.3.7                    py37_2    defaults
notebook                  5.6.0                    py37_0    defaults
numba                     0.39.0           py37h830ac7b_0    defaults
numexpr                   2.6.8            py37h9ef55f4_0    defaults
numpy                     1.15.1           py37ha559c80_0    defaults
numpy-base                1.15.1           py37h8128ebf_0    defaults
numpydoc                  0.8.0                    py37_0    defaults
odo                       0.5.1                    py37_0    defaults
olefile                   0.46                     py37_0    defaults
openpyxl                  2.5.6                    py37_0    defaults
openssl                   1.0.2p               hfa6e2cd_0    defaults
packaging                 17.1                     py37_0    defaults
pandas                    0.23.4           py37h830ac7b_0    defaults
pandoc                    1.19.2.1             hb2460c7_1    defaults
pandocfilters             1.4.2                    py37_1    defaults
parso                     0.3.1                    py37_0    defaults
partd                     0.3.8                    py37_0    defaults
path.py                   11.1.0                   py37_0    defaults
pathlib2                  2.3.2                    py37_0    defaults
patsy                     0.5.0                    py37_0    defaults
pep8                      1.7.1                    py37_0    defaults
pickleshare               0.7.4                    py37_0    defaults
pillow                    5.2.0            py37h08bbbbd_0    defaults
pip                       10.0.1                   py37_0    defaults
pkginfo                   1.4.2                    py37_1    defaults
pluggy                    0.7.1            py37h28b3542_0    defaults
ply                       3.11                     py37_0    defaults
prometheus_client         0.3.1            py37h28b3542_0    defaults
prompt_toolkit            1.0.15                   py37_0    defaults
pscondaenvs               1.2.4                ha00e74d_0    pscondaenvs
psutil                    5.4.7            py37hfa6e2cd_0    defaults
py                        1.6.0                    py37_0    defaults
pyasn1                    0.4.4            py37h28b3542_0    defaults
pyasn1-modules            0.2.2                    py37_0    defaults
pycodestyle               2.4.0                    py37_0    defaults
pycosat                   0.6.3            py37hfa6e2cd_0    defaults
pycparser                 2.18                     py37_1    defaults
pycrypto                  2.6.1            py37hfa6e2cd_9    defaults
pycurl                    7.43.0.2         py37h74b6da3_0    defaults
pyflakes                  2.0.0                    py37_0    defaults
pygments                  2.2.0                    py37_0    defaults
pylint                    2.1.1                    py37_0    defaults
pyodbc                    4.0.24           py37h6538335_0    defaults
pyopenssl                 18.0.0                   py37_0    defaults
pyparsing                 2.2.0                    py37_1    defaults
pyqt                      5.9.2            py37h6538335_2    defaults
pysocks                   1.6.8                    py37_0    defaults
pytables                  3.4.4            py37he6f6034_0    defaults
pytest                    3.8.0                    py37_0    defaults
pytest-arraydiff          0.2              py37h39e3cac_0    defaults
pytest-astropy            0.4.0                    py37_0    defaults
pytest-doctestplus        0.1.3                    py37_0    defaults
pytest-openfiles          0.3.0                    py37_0    defaults
pytest-remotedata         0.3.0                    py37_0    defaults
python                    3.7.0                hea74fb7_0    defaults
python-dateutil           2.7.3                    py37_0    defaults
python-libarchive-c       2.8                      py37_6    defaults
pytz                      2018.5                   py37_0    defaults
pywavelets                1.0.0            py37h452e1ab_0    defaults
pywin32                   223              py37hfa6e2cd_1    defaults
pywinpty                  0.5.4                    py37_0    defaults
pyyaml                    3.13             py37hfa6e2cd_0    defaults
pyzmq                     17.1.2           py37hfa6e2cd_0    defaults
qt                        5.9.6            vc14h1e9a669_2  [vc14]  defaults
qtawesome                 0.4.4                    py37_0    defaults
qtconsole                 4.4.1                    py37_0    defaults
qtpy                      1.5.0                    py37_0    defaults
requests                  2.19.1                   py37_0    defaults
rope                      0.11.0                   py37_0    defaults
ruamel_yaml               0.15.46          py37hfa6e2cd_0    defaults
scikit-image              0.14.0           py37h6538335_1    defaults
scikit-learn              0.19.2           py37heebcf9a_0    defaults
scipy                     1.1.0            py37h4f6bf74_1    defaults
seaborn                   0.9.0                    py37_0    defaults
send2trash                1.5.0                    py37_0    defaults
service_identity          17.0.0           py37h28b3542_0    defaults
setuptools                40.2.0                   py37_0    defaults
simplegeneric             0.8.1                    py37_2    defaults
singledispatch            3.4.0.3                  py37_0    defaults
sip                       4.19.8           py37h6538335_0    defaults
six                       1.11.0                   py37_1    defaults
snappy                    1.1.7                h777316e_3    defaults
snowballstemmer           1.2.1                    py37_0    defaults
sortedcollections         1.0.1                    py37_0    defaults
sortedcontainers          2.0.5                    py37_0    defaults
sphinx                    1.7.9                    py37_0    defaults
sphinxcontrib             1.0                      py37_1    defaults
sphinxcontrib-websupport  1.1.0                    py37_1    defaults
spyder                    3.3.1                    py37_1    defaults
spyder-kernels            0.2.6                    py37_0    defaults
sqlalchemy                1.2.11           py37hfa6e2cd_0    defaults
sqlite                    3.24.0               h7602738_0    defaults
statsmodels               0.9.0            py37h452e1ab_0    defaults
sympy                     1.1.1                    py37_0    defaults
tblib                     1.3.2                    py37_0    defaults
terminado                 0.8.1                    py37_1    defaults
testpath                  0.3.1                    py37_0    defaults
tk                        8.6.8                hfa6e2cd_0    defaults
toolz                     0.9.0                    py37_0    defaults
tornado                   5.1              py37hfa6e2cd_0    defaults
tqdm                      4.26.0           py37h28b3542_0    defaults
traitlets                 4.3.2                    py37_0    defaults
twisted                   18.7.0           py37hfa6e2cd_1    defaults
unicodecsv                0.14.1                   py37_0    defaults
urllib3                   1.23                     py37_0    defaults
vc                        14.1                 h0510ff6_4    defaults
vs2015_runtime            14.15.26706          h3a45250_0    defaults
wcwidth                   0.1.7                    py37_0    defaults
webencodings              0.5.1                    py37_1    defaults
werkzeug                  0.14.1                   py37_0    defaults
wheel                     0.31.1                   py37_0    defaults
widgetsnbextension        3.4.1                    py37_0    defaults
win_inet_pton             1.0.1                    py37_1    defaults
win_unicode_console       0.5                      py37_0    defaults
wincertstore              0.2                      py37_0    defaults
winpty                    0.4.3                         4    defaults
wrapt                     1.10.11          py37hfa6e2cd_2    defaults
xlrd                      1.1.0                    py37_1    defaults
xlsxwriter                1.1.0                    py37_0    defaults
xlwings                   0.11.8                   py37_0    defaults
xlwt                      1.3.0                    py37_0    defaults
xz                        5.2.4                h2fa13f4_4    defaults
yaml                      0.1.7                hc54c509_2    defaults
zeromq                    4.2.5                he025d50_1    defaults
zict                      0.1.3                    py37_0    defaults
zlib                      1.2.11               h8395fce_2    defaults
zope                      1.0                      py37_1    defaults
zope.interface            4.5.0            py37hfa6e2cd_0    defaults
@gwerbin
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gwerbin commented Oct 17, 2018

Update: it looks like the problem is resolved if I run activate base before running conda build. Evidently whatever was working for me before was fragile and I wasn't supposed to rely on it. Note that I have C:\Anaconda3 and C:\Anaconda3\Scripts in my user PATH.

@nehaljwani
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@gwerbin Running activate is necessary, as that sets the environment variables required for all packages in the environment to function properly. In the case of Windows, it sets the PATH properly to also include directories within that environment which contain the required DLLs.

Newer versions of Conda Build now depend on libarchive, that's why you were probably not seeing this error before.

mattwthompson added a commit to mattwthompson/mbuild that referenced this issue Dec 11, 2018
mattwthompson added a commit to mattwthompson/foyer that referenced this issue Dec 11, 2018
justinGilmer pushed a commit to mosdef-hub/mbuild that referenced this issue Dec 11, 2018
* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog
justinGilmer pushed a commit to mosdef-hub/foyer that referenced this issue Dec 18, 2018
* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Force Miniconda to a Python 3.6 version
justinGilmer pushed a commit to mosdef-hub/mbuild that referenced this issue Jan 7, 2019
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
justinGilmer pushed a commit to justinGilmer/mbuild that referenced this issue Jan 7, 2019
* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog
justinGilmer pushed a commit to justinGilmer/mbuild that referenced this issue Jan 7, 2019
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (mosdef-hub#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (mosdef-hub#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
justinGilmer added a commit to mosdef-hub/mbuild that referenced this issue Jan 8, 2019
* Fix too many files being left open in packing.py

`tempfile.mkstemp` provides a low level interface for interacting
with temporary files. However, garbage collection (closing files,
deleting files after use) must be manually taken care of.

Packing.py uses temp files when packing or solvating a system,
these files are never closed. This can cause the program to
reach the limit of open files for a process set by the OS level
`ulimit`.

These changes migrate from using `mkstemp` to a higher level interface
`tempfile.NamedTemporaryFile`, providing the same type of temporary
file, but with saner garbage collection and scope.

The sections where temp files are made are now contained in `try
finally` sections, to ensure proper file closure and deletion when the
program finishes, or is interrupted.

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* remove nested try-finally blocks

* Forgot to pass in path for the solvate method.

* Move file creation to method, move topology generation to file.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Update gitignore file for VSCode
Using Microsoft's VSCode generates an addtional directory
and files to assist the various plugins, save states, etc.

This is not needed for other users.

This has been added to the .gitignore file to prevent these files from
being committed erroneously.

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build` in Appveyor (#477)

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* GSD files now include 1,4 special pairs for use in OPLS (#473)

* Update dependency requirements (#457)

* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* Ensure all files generated in the for loops are closed and unlinked

* Increase the box dims for testing fill_region

a test for `fill_region` was packing a very small volume (~2nm^3)
with many water molecules. This led to parts of the molecules outside
the defined region. The region has been increased.

* Remove support for pytest-ignore-flaky

Recently, the tests on travis for the example notebooks
are failing due to some internal error with pytest-ignore-flaky
plugin.

It seems like the feature can be replicated well enough
using @pytest.mark.xfail with the strict setting to False.

* Update CI as well to remove 'pytest-ignore-flaky'

* Change the overlap parameter for a test, was causing floating point errors in PACKMOL

* Changelog.md

* Include information about the  in changelog.md
mikemhenry pushed a commit to mikemhenry/mbuild that referenced this issue Jan 28, 2019
* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog
mikemhenry pushed a commit to mikemhenry/mbuild that referenced this issue Jan 28, 2019
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (mosdef-hub#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (mosdef-hub#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
mikemhenry pushed a commit to mikemhenry/mbuild that referenced this issue Jan 28, 2019
* Fix too many files being left open in packing.py

`tempfile.mkstemp` provides a low level interface for interacting
with temporary files. However, garbage collection (closing files,
deleting files after use) must be manually taken care of.

Packing.py uses temp files when packing or solvating a system,
these files are never closed. This can cause the program to
reach the limit of open files for a process set by the OS level
`ulimit`.

These changes migrate from using `mkstemp` to a higher level interface
`tempfile.NamedTemporaryFile`, providing the same type of temporary
file, but with saner garbage collection and scope.

The sections where temp files are made are now contained in `try
finally` sections, to ensure proper file closure and deletion when the
program finishes, or is interrupted.

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* remove nested try-finally blocks

* Forgot to pass in path for the solvate method.

* Move file creation to method, move topology generation to file.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Update gitignore file for VSCode
Using Microsoft's VSCode generates an addtional directory
and files to assist the various plugins, save states, etc.

This is not needed for other users.

This has been added to the .gitignore file to prevent these files from
being committed erroneously.

* Fixes issues with packmol input files (mosdef-hub#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build` in Appveyor (mosdef-hub#477)

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* GSD files now include 1,4 special pairs for use in OPLS (mosdef-hub#473)

* Update dependency requirements (mosdef-hub#457)

* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (mosdef-hub#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (mosdef-hub#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* Ensure all files generated in the for loops are closed and unlinked

* Increase the box dims for testing fill_region

a test for `fill_region` was packing a very small volume (~2nm^3)
with many water molecules. This led to parts of the molecules outside
the defined region. The region has been increased.

* Remove support for pytest-ignore-flaky

Recently, the tests on travis for the example notebooks
are failing due to some internal error with pytest-ignore-flaky
plugin.

It seems like the feature can be replicated well enough
using @pytest.mark.xfail with the strict setting to False.

* Update CI as well to remove 'pytest-ignore-flaky'

* Change the overlap parameter for a test, was causing floating point errors in PACKMOL

* Changelog.md

* Include information about the  in changelog.md
umesh-timalsina pushed a commit to mosdef-hub/molbox that referenced this issue Jun 26, 2021
* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog
umesh-timalsina pushed a commit to mosdef-hub/molbox that referenced this issue Jun 26, 2021
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
umesh-timalsina pushed a commit to mosdef-hub/molbox that referenced this issue Jun 26, 2021
* Fix too many files being left open in packing.py

`tempfile.mkstemp` provides a low level interface for interacting
with temporary files. However, garbage collection (closing files,
deleting files after use) must be manually taken care of.

Packing.py uses temp files when packing or solvating a system,
these files are never closed. This can cause the program to
reach the limit of open files for a process set by the OS level
`ulimit`.

These changes migrate from using `mkstemp` to a higher level interface
`tempfile.NamedTemporaryFile`, providing the same type of temporary
file, but with saner garbage collection and scope.

The sections where temp files are made are now contained in `try
finally` sections, to ensure proper file closure and deletion when the
program finishes, or is interrupted.

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* remove nested try-finally blocks

* Forgot to pass in path for the solvate method.

* Move file creation to method, move topology generation to file.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Update gitignore file for VSCode
Using Microsoft's VSCode generates an addtional directory
and files to assist the various plugins, save states, etc.

This is not needed for other users.

This has been added to the .gitignore file to prevent these files from
being committed erroneously.

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build` in Appveyor (#477)

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* GSD files now include 1,4 special pairs for use in OPLS (#473)

* Update dependency requirements (#457)

* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* Ensure all files generated in the for loops are closed and unlinked

* Increase the box dims for testing fill_region

a test for `fill_region` was packing a very small volume (~2nm^3)
with many water molecules. This led to parts of the molecules outside
the defined region. The region has been increased.

* Remove support for pytest-ignore-flaky

Recently, the tests on travis for the example notebooks
are failing due to some internal error with pytest-ignore-flaky
plugin.

It seems like the feature can be replicated well enough
using @pytest.mark.xfail with the strict setting to False.

* Update CI as well to remove 'pytest-ignore-flaky'

* Change the overlap parameter for a test, was causing floating point errors in PACKMOL

* Changelog.md

* Include information about the  in changelog.md
umesh-timalsina pushed a commit to GOMC-WSU/MoSDeF-GOMC that referenced this issue Mar 22, 2022
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
umesh-timalsina pushed a commit to GOMC-WSU/MoSDeF-GOMC that referenced this issue Mar 22, 2022
* Fix too many files being left open in packing.py

`tempfile.mkstemp` provides a low level interface for interacting
with temporary files. However, garbage collection (closing files,
deleting files after use) must be manually taken care of.

Packing.py uses temp files when packing or solvating a system,
these files are never closed. This can cause the program to
reach the limit of open files for a process set by the OS level
`ulimit`.

These changes migrate from using `mkstemp` to a higher level interface
`tempfile.NamedTemporaryFile`, providing the same type of temporary
file, but with saner garbage collection and scope.

The sections where temp files are made are now contained in `try
finally` sections, to ensure proper file closure and deletion when the
program finishes, or is interrupted.

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* remove nested try-finally blocks

* Forgot to pass in path for the solvate method.

* Move file creation to method, move topology generation to file.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Update gitignore file for VSCode
Using Microsoft's VSCode generates an addtional directory
and files to assist the various plugins, save states, etc.

This is not needed for other users.

This has been added to the .gitignore file to prevent these files from
being committed erroneously.

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build` in Appveyor (#477)

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* GSD files now include 1,4 special pairs for use in OPLS (#473)

* Update dependency requirements (#457)

* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* Ensure all files generated in the for loops are closed and unlinked

* Increase the box dims for testing fill_region

a test for `fill_region` was packing a very small volume (~2nm^3)
with many water molecules. This led to parts of the molecules outside
the defined region. The region has been increased.

* Remove support for pytest-ignore-flaky

Recently, the tests on travis for the example notebooks
are failing due to some internal error with pytest-ignore-flaky
plugin.

It seems like the feature can be replicated well enough
using @pytest.mark.xfail with the strict setting to False.

* Update CI as well to remove 'pytest-ignore-flaky'

* Change the overlap parameter for a test, was causing floating point errors in PACKMOL

* Changelog.md

* Include information about the  in changelog.md
umesh-timalsina pushed a commit to umesh-timalsina/MoSDeF-GOMC that referenced this issue Oct 12, 2022
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
umesh-timalsina pushed a commit to umesh-timalsina/MoSDeF-GOMC that referenced this issue Oct 12, 2022
* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov
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