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Release bugfix version: 3.2.1 #158

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merged 153 commits into from
Nov 10, 2021
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a86144a
Move argparse customization to new file
blake-riley Sep 3, 2020
93f455f
Add formatter/action for --[no-]options to argparse
blake-riley Sep 3, 2020
1847422
Change all store_false actions with --no- to ToggleActionFlag type
blake-riley Sep 3, 2020
3efd5dd
Ensure long-form-arguments have dash-spacing, not underscore-spacing.…
blake-riley Sep 3, 2020
6274d96
Rename 'nowaters' variable to 'waters_clash', fix option
blake-riley Sep 3, 2020
ad344c0
(m) Remove full-stop from qfit protein argument help text
blake-riley Oct 12, 2020
6f68524
Update argparsing in qfit_residue
blake-riley Oct 12, 2020
a462fe1
Update argparsing in qfit_ligand
blake-riley Oct 12, 2020
060d4a6
Update examples in README to match argument availability
blake-riley Oct 12, 2020
c7e0fe7
Merge pull request #122 from ExcitedStates/hotfix/69-double-negatives…
blake-riley Nov 8, 2020
ab44318
Extend scale_rmask as option to user
blake-riley Nov 5, 2020
51c0e49
Extend option --sample-rotamers to user
blake-riley Nov 5, 2020
4b0418b
Add --random-seed flag, store value in options
blake-riley Nov 8, 2020
5dbe229
Build PRNG using the random-seed value, use it to source random numbers
blake-riley Nov 8, 2020
02f7707
Use a seeded PRNG in the relabeller
blake-riley Nov 8, 2020
e67320c
Bump numpy version requirements
blake-riley Nov 8, 2020
2a9f3d6
Merge pull request #124 from ExcitedStates/feature/random_seed
blake-riley Nov 8, 2020
9e89fe4
Added cryo-EM example
Nov 9, 2020
86f051b
adding qFit-ligand examples
Nov 9, 2020
438de5a
adding qFit-protein Cryo EM examples
Nov 9, 2020
8cac980
adding in RMSD option
Nov 9, 2020
e0f08f6
replacing hard coded RMSD cut off with option
Nov 9, 2020
c5f7b10
Merge pull request #126 from ExcitedStates/hotfix/qfit_ligand_RMSD
blake-riley Nov 9, 2020
3286da0
Changing variable name to match qfit_protein
Nov 13, 2020
68c7158
Update main.yml
Nov 20, 2020
1285d84
Merge pull request #129 from ExcitedStates/hotfix/update_minicondasetup
blake-riley Nov 20, 2020
12f47b8
Update b_factor.py
Dec 8, 2020
61cfa1d
Update main.yml
Jan 8, 2021
973654a
Create environment.yml
Jan 8, 2021
5f8e336
Update main.yml
Jan 8, 2021
7394b83
Update main.yml
Jan 8, 2021
42d7c94
Update main.yml
Jan 8, 2021
17d62be
trying to get tox to work
Jan 8, 2021
9ec9842
Update main.yml
Jan 8, 2021
8211dee
Update main.yml
Jan 8, 2021
93e6a9a
adding pytest to environment
Jan 8, 2021
7ac31eb
fixing spelling of files
Jan 8, 2021
56b9a61
updating using pytest
Jan 8, 2021
223966b
updating indents
Jan 9, 2021
818df77
adding python version
Jan 9, 2021
1a50a54
Update main.yml
Jan 9, 2021
7c7ece6
updating conda install
Jan 9, 2021
eaddd81
Update main.yml
Jan 12, 2021
bbf718b
Update main.yml
Jan 12, 2021
e43e9d9
update to s-weighand
Jan 12, 2021
ef228dd
re-starting pytest
Jan 12, 2021
f3f592b
Update main.yml
Jan 12, 2021
eb07dbb
Update main.yml
Jan 12, 2021
5ddb183
Update main.yml
Jan 12, 2021
3d31afc
moving env file
Jan 12, 2021
53a7471
Update main.yml
Jan 12, 2021
d68dc1d
Update main.yml
Jan 12, 2021
6cf6b81
Rename environment.yml to ect/environment.yml
Jan 12, 2021
6f8fc54
Update main.yml
Jan 12, 2021
806efa8
Update main.yml
Jan 12, 2021
3f21ae7
Update main.yml
Jan 12, 2021
8eee21e
Rename environment.yml to env.yml
Jan 12, 2021
56368b8
Update main.yml
Jan 12, 2021
1a54173
Update main.yml
Jan 13, 2021
d678848
Rename ect/env.yml to env.yml
Jan 13, 2021
1195807
Update main.yml
Jan 13, 2021
f36644e
Update main.yml
Jan 13, 2021
a20adf9
Update env.yml
Jan 13, 2021
525b098
Update main.yml
Jan 13, 2021
28a15a5
Update main.yml
Jan 13, 2021
2627638
Update env.yml
Jan 13, 2021
57c91b7
Update main.yml
Jan 13, 2021
10f418b
Update test_qfit_protein.py
Jan 13, 2021
de651d3
Update test_qfit_protein.py
Jan 13, 2021
0931944
Update main.yml
Jan 13, 2021
bfa2ed8
Update main.yml
Jan 13, 2021
32fdab6
Update test_qfit_protein.py
Jan 13, 2021
6f3bb92
Update main.yml
Jan 13, 2021
3a31653
Update test_qfit_protein.py
Jan 13, 2021
8cf689b
Update test_qfit_protein.py
Jan 13, 2021
9e14795
Update test_qfit_protein.py
Jan 13, 2021
18bbe94
Update test_qfit_ligand.py
Jan 13, 2021
c114980
Update test_qfit_protein.py
Jan 13, 2021
66f3721
Update test_qfit_ligand.py
Jan 13, 2021
00aead7
Update main.yml
Jan 13, 2021
c927c11
Update test_qfit_protein.py
Jan 13, 2021
c6e8d34
Update test_qfit_protein.py
Jan 13, 2021
c73bf3f
removing tox.ini since we are using pymol
Jan 13, 2021
0f638cf
Add pipefail to bash command.
Jan 15, 2021
7197420
adding trailing comma.
Jan 15, 2021
1110820
adding trailing comma
Jan 15, 2021
668577e
Merge pull request #137 from ExcitedStates/fixing_CI_tests
Jan 15, 2021
e6c084c
Merge pull request #127 from ExcitedStates/hotfix/write_typo
Jan 15, 2021
be56758
Update b_factor.py
Jan 15, 2021
36ead88
Merge pull request #131 from ExcitedStates/feature/post_scripts
Jan 15, 2021
49ac837
Merge pull request #125 from ExcitedStates/adding_examples
Jan 15, 2021
43189db
(m) Use standard filename: environment.yml
blake-riley May 13, 2021
321fd05
Make CI test against this branch
blake-riley May 12, 2021
a7ee1fe
[DEBUG] Query the numpy versions at different stages of build process
blake-riley May 12, 2021
7a48a69
Use --no-build-isolation install in CI script (fix numpy C-API crash)
blake-riley May 13, 2021
139af48
Limit numpy upper version in both _build_ and _install_ sections
blake-riley Sep 9, 2021
30b88a2
Revert "[DEBUG] Query the numpy versions at different stages of build…
blake-riley Sep 9, 2021
68b6375
Revert "Make CI test against this branch"
blake-riley Sep 9, 2021
d4d7a9e
Merge pull request #148 from ExcitedStates/hotfix/fixCI
blake-riley Sep 9, 2021
e18aefc
Add pandas to requirements
blake-riley Sep 9, 2021
ee0e6a2
Update docstring for get_metrics.py & argparse formatting
blake-riley Mar 15, 2021
f585ab1
(m) pep8 spacing
blake-riley Mar 15, 2021
f900475
Strip amide H before calculating RMSF (necessary b/c of backbone-H bug)
blake-riley Mar 15, 2021
ca441d5
Strip all H before calculating RMSF
blake-riley May 11, 2021
ea5c620
Refactor get_metrics.py
blake-riley May 11, 2021
e4705bf
Merge refactored get_metrics.py script into analysis
blake-riley Sep 10, 2021
31b3d26
Update qfit_RMSF.py
Jan 23, 2021
6ac6db0
Fix SyntaxError bug
blake-riley Mar 15, 2021
c840406
Simplify string handling in qfit_RMSF.py
blake-riley Mar 15, 2021
1b36fd0
(m) Cleanup spacing
blake-riley Sep 9, 2021
36814c3
(m) Compare with None using 'is' not '=='
blake-riley Sep 9, 2021
7286598
(m) Remove unused variables, avoid overwriting builtins
blake-riley Sep 9, 2021
9fa9e20
(m) Remove unused imports
blake-riley Sep 9, 2021
5a2af22
Merge patches to qfit_RMSF.py
blake-riley Sep 10, 2021
c298abe
Remove unused imports, make sure all scripts start with shabang
Jan 24, 2021
d3bea9e
(m) Clean up spacing
blake-riley Sep 10, 2021
baf4e8b
(m) Compare to None with 'is', not '=='
blake-riley Sep 10, 2021
da2e23c
(m) Remove unused variables, use unique variable names
blake-riley Sep 10, 2021
3c7faee
Merge patches to b_factor.py
blake-riley Sep 10, 2021
59e9de0
(m) Clean up spacing, fix typo
blake-riley Sep 10, 2021
860d7b6
(m) Compare to None with 'is', not '=='
blake-riley Sep 10, 2021
1a7c446
(m) Remove unused imports, make sure all scripts start with shabang
blake-riley Sep 10, 2021
11bf7a4
Merge patches to other analysis scripts
blake-riley Sep 10, 2021
9e4d368
Trust user-provided ligand names (assume match to CCP4 monomer library)
blake-riley May 12, 2021
167b73e
Add ligand occupancy script
Sep 8, 2021
8c41a9b
adding alpha rmsd script
Sep 8, 2021
3092663
adding re-order PDB script
Sep 10, 2021
aeb55bd
adding water stats script
Sep 10, 2021
0adb1d4
Bugfix?: Comment out missing function
blake-riley Sep 9, 2021
7530d24
Add relabeling chain script
Sep 10, 2021
16798d5
adding water clashing script
Sep 8, 2021
5ea277e
Merge pull request #146 from ExcitedStates/analysis
blake-riley Sep 16, 2021
70b0df8
correcting line for post qFit refine cryoEM
Sep 27, 2021
ff939e3
Merge pull request #152 from ExcitedStates/hotfix/cryoEM_refine_corre…
blake-riley Sep 27, 2021
9c4dce6
Fixup indentation in alpha_rmsd
blake-riley Sep 23, 2021
3b4a6c8
adding qfit_protein for scale/cryst
Sep 23, 2021
870ed85
adding amended structure files
Sep 23, 2021
2aac1d6
Merge pull request #155 from ExcitedStates/hotfix/fix-indent
blake-riley Nov 2, 2021
9d43949
Merge pull request #151 from ExcitedStates/PDB_header_redo
blake-riley Nov 2, 2021
21d2779
Add vscode to gitignore
blake-riley Sep 8, 2021
62393fd
Add vscode development configs
blake-riley Sep 11, 2021
4e26a37
Install development requirements on container creation
blake-riley Sep 11, 2021
08b204d
Add linting config
blake-riley Sep 11, 2021
3f0a4e5
Customize linter warnings
blake-riley Sep 9, 2021
78f7d82
Add vscode config into shared repo
blake-riley Nov 2, 2021
49aa8f9
Shift to minimum python 3.7, numpy version increase to 1.20, use cond…
blake-riley Sep 10, 2021
7b6c828
Remove deprecated numpy dtype
blake-riley Sep 10, 2021
67176be
Fix slice type: we just want to slice with a simple iterator
blake-riley Nov 2, 2021
92e493d
Merge pull request #156 from ExcitedStates/feature/bump_python_reqs
blake-riley Nov 8, 2021
097f183
Remove redundant licence from top of files
blake-riley Sep 21, 2021
d29fa61
Add citation to README
blake-riley Sep 21, 2021
2dfcd3a
Merge pull request #157 from ExcitedStates/hotfix/licence_cite
blake-riley Nov 9, 2021
67da707
Release v3.2.1 (bugfixes)
blake-riley Nov 10, 2021
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Use --no-build-isolation install in CI script (fix numpy C-API crash)
Without this option, pip will go fetch all the install_requires listed
in setup.py for an isolated build. The problem is that the version of
numpy it grabs could be different to one that is _already_ present in
the conda env.

Since numpy _is_ already present in the conda env, we expose it to pip
using the --no-build-isolation flag. This way, our C extension is built
against the same numpy as will be present in the conda env.

This is particularly important given numpy 1.20 has recently shifted
API version (see numpy/numpy/core/include/numpy/numpyconfig.h,
numpy/numpy/core/code_generators/cversions.txt).
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blake-riley committed Sep 9, 2021
commit 7a48a69718525faac053aa2f44102f2583c698d8
2 changes: 1 addition & 1 deletion .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,6 @@ jobs:
- name: Run pytest with the Conda environment
shell: bash -l -o pipefail {0}
run: |
pip install -v .
pip install --no-build-isolation -v .
conda install pytest
pytest