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add h5py to setup.py's extra_requires #3711

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merged 11 commits into from
Jul 6, 2022
Merged

add h5py to setup.py's extra_requires #3711

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ff3996b
add h5py to setup.py's extra_requires
orbeckst Jun 9, 2022
e104b32
minimum h5py >= 2.10
orbeckst Jun 9, 2022
6c4bd16
update extra_deps in setup.py
orbeckst Jun 9, 2022
a7bc680
updated CHANGELOG
orbeckst Jun 9, 2022
ded6679
pep8 fixes
orbeckst Jun 10, 2022
1762aad
updated sklearn --> scikit-learn in setup.py
orbeckst Jun 10, 2022
752890a
Update package/CHANGELOG
orbeckst Jun 11, 2022
7bf94a9
deprecate extras_require "AMBER" target for 2.4
orbeckst Jun 11, 2022
4a12625
Merge branch 'develop' into h5py-extradep
IAlibay Jun 13, 2022
78ae314
Merge branch 'develop' into h5py-extradep
orbeckst Jul 5, 2022
afb49ee
Merge branch 'develop' into h5py-extradep
IAlibay Jul 5, 2022
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2 changes: 1 addition & 1 deletion .github/actions/setup-deps/action.yaml
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Expand Up @@ -54,7 +54,7 @@ inputs:
clustalw:
default: 'clustalw=2.1'
h5py:
default: 'h5py'
default: 'h5py>=2.10'
joblib:
default: 'joblib>=0.12'
netcdf4:
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2 changes: 1 addition & 1 deletion azure-pipelines.yml
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Expand Up @@ -92,7 +92,7 @@ jobs:
pytest-xdist
scikit-learn
scipy
h5py
h5py>=2.10
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Let's leave it as this for now, long term we might want to come back and put minimum pins on stuff here too (although to be honest we'll just pick up the maximum version here anyways, I guess I'm just being too pedantic...)

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I understand your comment as "h5py>=2.10 is fine for now" so I am not changing it.

tqdm
threadpoolctl
fasteners
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2 changes: 1 addition & 1 deletion maintainer/conda/environment.yml
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Expand Up @@ -9,7 +9,7 @@ dependencies:
- fasteners
- griddataformats
- gsd
- h5py
- h5py>=2.10
- hypothesis
- joblib>=0.12
- matplotlib==3.2.2
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5 changes: 5 additions & 0 deletions package/CHANGELOG
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Expand Up @@ -29,12 +29,17 @@ Enhancements
(CZI Performance track, PR #3683)

Changes
* To add additional optional packages for different file formats when
using `pip` use the new "extra_formats" extras_require target as in
`pip install ./package[extra_formats]` (Issue #3701, PR #3711)
* Minimum supported NumPy version is now 1.20 (1.21 for macosx-arm64)
as per NEP29 (PR #3737)
* Narrowed variable scope to reduce use of OpenMP `private` clause (PR #3706, PR
#3728)

Deprecations
* The extras_requires target "AMBER" for `pip install ./package[AMBER]`
will be removed in 2.4. Use "extra_formats". (Issue #3701, PR #3711)
* Deprecate `density` parameter in favor of `norm` in InterRDF_s
(Issue #3687)

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22 changes: 10 additions & 12 deletions package/setup.py
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Expand Up @@ -63,15 +63,8 @@
print('Please upgrade your version of Python.')
sys.exit(-1)

if sys.version_info[0] < 3:
import ConfigParser as configparser
else:
import configparser

if sys.version_info[0] >= 3:
from subprocess import getoutput
else:
from commands import getoutput
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import configparser
from subprocess import getoutput

# NOTE: keep in sync with MDAnalysis.__version__ in version.py
RELEASE = "2.3.0-dev0"
Expand Down Expand Up @@ -654,14 +647,19 @@ def long_description(readme):
# you might prefer to use the version available through your
# packaging system
extras_require={
'AMBER': [
'AMBER': [ # REMOVE for 2.4.0, use 'extra_formats'
'netCDF4>=1.0', # for fast AMBER writing, also needs HDF5
],
'extra_formats': [ # additional file formats
'netCDF4>=1.0', # for fast AMBER writing, also needs HDF5
'h5py>=2.10', # H5MD
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'chemfiles>=0.10', # multiple formats supported by chemfiles
],
'analysis': [
'seaborn', # for annotated heat map and nearest neighbor
# plotting in PSA
'sklearn', # For clustering and dimensionality reduction
# functionality in encore
'scikit-learn', # For clustering and dimensionality
# reduction functionality in encore
'tidynamics>=1.0.0', # For MSD analysis method
],
},
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