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Add CI caching for python environments #23

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merged 38 commits into from
Apr 30, 2021
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582a178
Added first pytest script for protein class and a script for performi…
okkevaneck Apr 19, 2021
9cc0e0e
Added pytest in CI
okkevaneck Apr 19, 2021
2145237
Forgot -r for file
okkevaneck Apr 19, 2021
7c0e560
Version of pytest with pytest at end of pipeline
okkevaneck Apr 21, 2021
f4f4612
New pytest CI where pip installs local package
okkevaneck Apr 21, 2021
11708f3
Fixed tabs and added caching of python/pip environment
okkevaneck Apr 21, 2021
7f5e83d
Removed dot and added removal of build dirs to manage clean command
okkevaneck Apr 21, 2021
749b578
Added cache ignores for env setup and ids for the caches
okkevaneck Apr 21, 2021
a12bb08
Fixed cache IDs
okkevaneck Apr 21, 2021
53bae23
Renamed cache because GitHub does not allow for clearing caches...
okkevaneck Apr 21, 2021
7d23e77
Moved python setup to be before cache loading
okkevaneck Apr 21, 2021
b1595aa
Run that will install the dependencies
okkevaneck Apr 21, 2021
625d51e
Uncommented the cache-hit detection for installing dependencies
okkevaneck Apr 21, 2021
f917b13
Updated pre-commit version in hope that runner will create new cache
okkevaneck Apr 21, 2021
69ea8d8
Added more tests and added flake8 incompatability
okkevaneck Apr 21, 2021
73aae44
Other flake8 config try
okkevaneck Apr 21, 2021
767ab98
Reset to .flake8 file
okkevaneck Apr 21, 2021
6fbbf6b
Downgrade of pre-commit to force dep. installation in CI
okkevaneck Apr 21, 2021
c5f4139
Different pre-commit version
okkevaneck Apr 21, 2021
4f23882
Added depth_first tests
okkevaneck Apr 21, 2021
8f5a567
Added depth_first_bnb tests
okkevaneck Apr 21, 2021
d59855d
Push to try and install all dependencies correctly
okkevaneck Apr 29, 2021
9af7093
Added back cache check for installing dependencies. New way of callin…
okkevaneck Apr 29, 2021
e036f43
Removed ls
okkevaneck Apr 29, 2021
64440a0
Core change test
okkevaneck Apr 29, 2021
762576f
Core change test - new correctly
okkevaneck Apr 29, 2021
1c363b4
Core archiving works
okkevaneck Apr 29, 2021
a23df3c
Fixed pytest ordering and upgraded pandas version to trigger new cache
okkevaneck Apr 29, 2021
4b17ba6
Upgraded pandas
okkevaneck Apr 29, 2021
616f3ef
Changed pandas version to 1.1.0
okkevaneck Apr 29, 2021
7e06ce1
Dependency check
okkevaneck Apr 29, 2021
53e4766
new flake8 installation
okkevaneck Apr 29, 2021
050f1e8
Flake8 action
okkevaneck Apr 29, 2021
935ed11
Added pip update flag
okkevaneck Apr 29, 2021
3c63847
Cleaned up the flake8 action usage
okkevaneck Apr 29, 2021
5704f7c
Trying to install new deps
okkevaneck Apr 29, 2021
585a431
Removed caching, only using dependencies during pytest
okkevaneck Apr 29, 2021
43f2425
Merged with develop
okkevaneck Apr 30, 2021
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29 changes: 10 additions & 19 deletions .github/workflows/build_deploy.yml
Original file line number Diff line number Diff line change
Expand Up @@ -22,29 +22,21 @@ jobs:
syntax_check:
name: Check for syntax errors
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.6]
os: [ubuntu-latest, windows-latest, macos-latest]
steps:
- uses: actions/checkout@v2

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
- name: Flake8 - Error on syntax errors or undefined names
uses: py-actions/flake8@v1.1.0
with:
python-version: ${{ matrix.python-version }}
args: --count --select=E9,F63,F7,F82 --show-source --statistics
update-pip: "true"

- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8

- name: Lint with flake8
run: |
# Stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# Exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Flake8 - Warn on everything else
uses: py-actions/flake8@v1.1.0
with:
args: --count --exit-zero --max-complexity=10 --statistics
max-line-length: 127
update-pip: "true"

pytest:
name: Pytest
Expand All @@ -71,7 +63,6 @@ jobs:
- name: Test with pytest
run: pytest


build_wheels:
name: Build wheels
needs: [pytest, matrix_prep]
Expand Down