230 basic linting

.github/workflows/_run_tests.yml

@@ -0,0 +1,46 @@
+# reusable workflow to run tests on different installation types and OS
+name: run-tests
+
+on:
+ workflow_call:
+ inputs:
+ os:
+ required: true
+ type: string
+ python-version:
+ required: true
+ type: string
+ install-script:
+ required: true
+ type: string
+ test-script:
+ required: true
+ type: string
+jobs:
+ run-unit-tests-stable-ubuntu:
+ runs-on: ${{ inputs.os }}
+ steps:
+ - uses: actions/checkout@v4
+ - uses: conda-incubator/setup-miniconda@v3
+ with:
+ miniconda-version: "latest"
+ auto-update-conda: true
+ python-version: ${{ inputs.python-version }}
+ - name: Setup pip cache
+ uses: actions/cache@v4
+ with:
+ path: ~/.cache/pip
+ key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+ - name: Conda info
+ shell: bash -l {0}
+ run: conda info
+ - name: Perform pip installation with all stable dependencies
+ shell: bash -l {0}
+ run: |
+ cd misc
+ . ./${{ inputs.install-script }}
+ - name: Run tests
+ shell: bash -l {0}
+ run: |
+ cd tests
+ . ./${{ inputs.test-script }}

.github/workflows/branch-checks.yaml

@@ -0,0 +1,26 @@
+# checks to run on branches for each pull request
+name: branch-checks
+
+on:
+ pull_request:
+
+jobs:
+ pre-commit:
+ name: Run all pre-commit hooks
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v3
+ - uses: actions/setup-python@v3
+ - uses: pre-commit/[email protected]
+ # For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
+ run-tests-stable:
+ name: Test stable pip installation on ubuntu-latest
+ strategy:
+ matrix:
+ os: [ubuntu-latest]
+ uses: ./.github/workflows/_run_tests.yml
+ with:
+ python-version: ${{ matrix.python-version }}
+ os: ${{ matrix.os }}
+ install-script: ./pip_install.sh stable,test
+ test-script: ./run_unit_tests.sh

.github/workflows/pip_installation.yml

@@ -1,71 +1,45 @@
+# Perform pip installation (stable, loose) and run tests on all three OS
+
+# For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
+# On each push to develop, the whole test matrix runs, additionally, its success is mandatory for merging to main.
+# In the (assumed to be rare case) that these full matrix tests fail but the reduced matrix tests passed,
+# we will learn about it latest before pushing to main. The merge that caused the issue can then be identified
+# from the tests that ran on develop.
+
 on:
+ push:
+ branches: [ main, development ]
  pull_request:
+ branches: [ main ]
  workflow_dispatch:
 
-name: Perform installation and run tests
+name: Perform pip installation and run unit tests
 
 concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
- cancel-in-progress: true
+ cancel-in-progress: false
 
 jobs:
- stable_installation:
- name: Test stable pip installation on ${{ matrix.os }}
- runs-on: ${{ matrix.os }}
+ run-unit-tests-stable:
+ name: Test stable pip installation on 3 OS
+ strategy:
+ matrix:
+ os: [ubuntu-latest, macos-13, windows-latest]
+ uses: ./.github/workflows/_run_tests.yml
+ with:
+ python-version: ${{ matrix.python-version }}
+ os: ${{ matrix.os }}
+ install-script: ./pip_install.sh stable,test
+ test-script: ./run_unit_tests.sh
+
+ run-unit-tests-loose:
+ name: Test loose pip installation on 3 OS
  strategy:
  matrix:
- os: [ubuntu-latest, macos-13, windows-latest]
- steps:
- - uses: actions/checkout@v4
- - name: Setup pip cache
- uses: actions/cache@v3
- with:
- path: ~/.cache/pip
- key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
- - uses: conda-incubator/setup-miniconda@v3
- with:
- auto-update-conda: true
- python-version: ${{ matrix.python-version }}
- - name: Conda info
- shell: bash -l {0}
- run: conda info
- - name: Test pip installation with all stable dependencies
- shell: bash -l {0}
- run: |
- cd misc
- . ./pip_install.sh stable,test
- - name: Unittests
- shell: bash -l {0}
- run: |
- cd tests
- . ./run_unit_tests.sh
-# loose_installation:
-# name: Test loose pip installation on ${{ matrix.os }}
-# runs-on: ${{ matrix.os }}
-# strategy:
-# matrix:
-# os: [ubuntu-latest, macos-13, windows-latest]
-# steps:
-# - uses: actions/checkout@v4
-# - name: Setup pip cache
-# uses: actions/cache@v3
-# with:
-# path: ~/.cache/pip
-# key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
-# - uses: conda-incubator/setup-miniconda@v3
-# with:
-# auto-update-conda: true
-# python-version: ${{ matrix.python-version }}
-# - name: Conda info
-# shell: bash -l {0}
-# run: conda info
-# - name: Test pip installation with all loose dependencies
-# shell: bash -l {0}
-# run: |
-# cd misc
-# . ./pip_install.sh loose,test
-# - name: Unittests
-# shell: bash -l {0}
-# run: |
-# cd tests
-# . ./run_unit_tests.sh
+ os: [ ubuntu-latest, macos-13, windows-latest ]
+ uses: ./.github/workflows/_run_tests.yml
+ with:
+ python-version: ${{ matrix.python-version }}
+ os: ${{ matrix.os }}
+ install-script: ./pip_install.sh test
+ test-script: ./run_unit_tests.sh

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
  - id: end-of-file-fixer
  - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.4.0
+ rev: v0.4.9
  hooks:
  - id: ruff-format
  #- id: ruff

alphadia/grouping.py

@@ -22,7 +22,7 @@ def group_and_parsimony(
  ----------
  precursor_idx : np.array[int]
  Array containing unique integer indices corresponding to each peptide precursor
- precursor_ids : np.array[str] 
+ precursor_ids : np.array[str]
  Array of variable length semicolon separated str belonging to a given peptide precursor id
 
  Returns
@@ -91,7 +91,7 @@ def group_and_parsimony(
  # check that all return_dict keys are unique. Assume same length and unique keys constitutes match to precursor_idx
  if len(return_dict) != len(set(return_dict.keys())):
  raise ValueError(
- """Not all precursors were found in the output of the grouping function. 
+ """Not all precursors were found in the output of the grouping function.
  Duplicate precursors were found."""
  )
 
@@ -125,7 +125,7 @@ def perform_grouping(
 
  Returns
  -------
- pd.DataFrame : 
+ pd.DataFrame :
  Precursor table with grouped proteins
 
  """
@@ -144,7 +144,7 @@ def perform_grouping(
  # TODO: consider removing check for duplicates since duplicate masking is implemented above
  if upsm.duplicated(subset=["precursor_idx"]).any():
  raise ValueError(
- """The same precursor was found annotated to different proteins. 
+ """The same precursor was found annotated to different proteins.
  Please make sure all precursors were searched with the same library."""
  )
 

alphadia/outputaccumulator.py

@@ -168,7 +168,9 @@ def parse_output_folder(
 
  # ----------------- Fragment -----------------
  # Filer fragments that are not used in the precursors
- frag_df = frag_df[frag_df["precursor_idx"].isin(self._precursor_df["precursor_idx"])]
+ frag_df = frag_df[
+ frag_df["precursor_idx"].isin(self._precursor_df["precursor_idx"])
+ ]
  self._fragment_df = frag_df[
  ["mz", "intensity", "precursor_idx", "frag_idx", "correlation"]
  ].copy()