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Rework Documentation #233

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Jul 20, 2024
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2a42bc0
Pytest all modules
thalassemia Jul 3, 2024
b85ed33
Add pytest coverage comment on PRs
thalassemia Jul 4, 2024
cb4852c
Import biology module before nextflow
thalassemia Jul 4, 2024
f1bc182
Clean up ecoli_master_sim CLI
thalassemia Jul 11, 2024
926a20d
Unnest parquet emitter config options
thalassemia Jul 11, 2024
7f89d01
Move PR CI tests to Github Actions
thalassemia Jul 11, 2024
91aea9d
Automatically run analysis scripts on all possible cell subsets for u…
thalassemia Jul 12, 2024
7a4bd34
Remove raw_output check
thalassemia Jul 12, 2024
bdab403
Fix data filter handling for string Hive columns
thalassemia Jul 12, 2024
80e7f59
Separate config file for two generation test
thalassemia Jul 12, 2024
ae6c874
Get rid of unused Clickhouse emitter
thalassemia Jul 13, 2024
b8f65b2
Fix a bunch of Sphinx issues
thalassemia Jul 13, 2024
b69575d
Get rid of old tutorial notebooks
thalassemia Jul 13, 2024
af9cdfe
Fix PR test YAML
thalassemia Jul 13, 2024
c42340d
Setup new documentation skeleton
thalassemia Jul 14, 2024
dad1abb
Ruff format
thalassemia Jul 14, 2024
967aa80
Fix manual variable time stepping
thalassemia Jul 16, 2024
02f01cd
Fix topology plot
thalassemia Jul 16, 2024
ece0ba8
Lots of documentation
thalassemia Jul 17, 2024
c8af073
Deprecate -c in favor of --config everywhere
thalassemia Jul 18, 2024
df2833f
Documentation fixes
thalassemia Jul 18, 2024
98ffa81
Folder for all analysis types with brief descriptions
thalassemia Jul 18, 2024
2e8ca0e
variant_names argument for analysis scripts maps experiment IDs to va…
thalassemia Jul 18, 2024
a18ce3a
Save analysis output to Hive partitioned directory structure in outdir
thalassemia Jul 18, 2024
f5238aa
More work on documentation
thalassemia Jul 18, 2024
ad602f2
Omit data__ prefix for config Parquet column names
thalassemia Jul 20, 2024
596cb88
More documentation work
thalassemia Jul 20, 2024
a74ef6b
Add some information about cross-links and type hints in documentation
thalassemia Jul 20, 2024
214f1a1
Fix reproducibility and two-generation GitHub Actions
thalassemia Jul 20, 2024
7a1104b
Fix mypy error
thalassemia Jul 20, 2024
bebe4da
Runscripts accept --config not -c
thalassemia Jul 20, 2024
d991915
More fixes for new GitHub Actions
thalassemia Jul 20, 2024
4ab9349
Try more fixes
thalassemia Jul 20, 2024
0519615
Fix no_suffix_time CLI option
thalassemia Jul 20, 2024
bc04111
Set no_suffix_time to False by default
thalassemia Jul 20, 2024
9184796
Get rid of no_suffix_time option
thalassemia Jul 20, 2024
f45827c
Handle experiment ID suffix in reproducibility test
thalassemia Jul 20, 2024
8ab39dd
Create Hive partition for experiment schema if not exists
thalassemia Jul 20, 2024
79f19bf
Try removing fg
thalassemia Jul 20, 2024
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Pytest all modules
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thalassemia committed Jul 3, 2024
commit 2a42bc060d471bcb9c5d2ba4109280084b1043f5
2 changes: 1 addition & 1 deletion .github/workflows/pytest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ jobs:
make clean compile
- name: Test with pytest
run: |
python -m pytest --cov=ecoli --durations=0
python -m pytest --cov=ecoli --cov=reconstruction --cov=wholecell --cov=runscripts --durations=0
Mypy:
runs-on: ubuntu-latest
strategy:
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6 changes: 4 additions & 2 deletions pytest.ini
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
[pytest]
python_files = *.py
addopts = --doctest-modules --strict-markers
addopts = --doctest-modules --strict-markers --ignore=wholecell/utils/_netflow
testpaths =
ecoli
migration
scripts
runscripts
wholecell
reconstruction
markers =
slow: indicates slow tests (deselect with '-m "not slow"')
noci: indicates tests that should not run on CI (e.g. because they are too slow)
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1 change: 1 addition & 0 deletions requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@ jupyterlab_widgets==3.0.11
kiwisolver==1.4.5
lazy_loader==0.4
libpysal==4.11.0
line_profiler==4.1.3
linkify-it-py==2.0.3
llvmlite==0.43.0
logical-unification==0.4.6
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2 changes: 1 addition & 1 deletion wholecell/tests/utils/test_fast_nnls.py
Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ def test_full_sparse_equivalence(self):
x2, r2 = fast_nnls(sA, b)

npt.assert_array_equal(x1, x2)
npt.assert_array_equal(r1, r2)
npt.assert_array_almost_equal(r1, r2)

def test_reproducibility(self):
"""
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