Merge branch 'corems_4_0' into 'master'

CoreMS 4.0 release

Closes #218

See merge request mass-spectrometry/corems!211

Author: corilo

.bumpversion.cfg

@@ -1,18 +1,9 @@
 [bumpversion]
-current_version = 3.11.0
+current_version = 4.0.0
 commit = False
 tag = False
 
-[bumpversion:part:release]
-optional_value = beta
-values = 
-	alpha
-	beta
-	rc1
-	rc2
-	rc3
-
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
 [bumpversion:file:README.md]
 

.bumpversion.toml

@@ -0,0 +1,51 @@
+name: Test
+
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'doc/**'
+      - '**/*.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'doc/**'
+      - '**/*.md'
+
+concurrency:
+  group: test-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Source tests
+            make_target: ci-test-source
+          - name: Notebook tests
+            make_target: ci-test-notebooks
+    env:
+      DOTNET_SYSTEM_GLOBALIZATION_INVARIANT: '1'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
+
+      - name: Set up Python
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5
+        with:
+          python-version: '3.13'
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Set up .NET
+        uses: actions/setup-dotnet@67a3573c9a986a3f9c594539f4ab511d57bb3ce9  # v4
+        with:
+          dotnet-version: '8.0'
+
+      - name: Run tests
+        run: make ${{ matrix.make_target }} SKIP_LIPIDOMICS_DB=1 SKIP_MOLECULAR_DB=1

.github/workflows/pypi_publish.yml

@@ -1,90 +1,114 @@
+# Virtual environments
 env/
-venv/ 
-test_env/ 
+venv/
+test_env/
 venv310/
 venvwsl/
-tmp_data/ 
-tmp_docs/
-.pyc  
+.venv/
+core_env/
+
+# Python artifacts and caches
+.pyc
 .pyo
-*.hdf5
-*.d  
-tmp_data/
-*.so  
-*.pkl  
-*.ems
-*.sqlite
-pyvenv.cfg  
-.DS_Store 
-__pycache__/  
-res/  
-doc/coverage_html_report
-corems.egg-info/  
-corems/libs/  
-core_env/  
-molformula-data/
-.vscode/  
+__pycache__/
 .pytest_cache/
-.vs/
-res/data/
+.pytest_tmp/
+.ipynb_checkpoints/
 .eggs/
-dist/
+*.egg*
+pyvenv.cfg
+
+# Build outputs and binary artifacts
 build/
-.ipynb_checkpoints/
-.pytest_cache/
+dist/
+*.d
+*.so
+*.pkl
+*.ems
+*.sqlite
+*.hdf5
+
+# IDE/editor and OS files
+.vscode/
+.vs/
+.DS_Store
+
+# Project temp and local config
+tmp_data/
+tmp_docs/
+results/
+dev/
+clr_test/
+r00*/
+config.yaml
+*.token
 .coverage
+.pypirc
+
+# Project folders
+res/
+res/data/
+doc/coverage_html_report
+corems.egg-info/
+corems/libs/
+molformula-data/
+
+# ext_lib exceptions
+ext_lib/
+!ext_lib/ChemstationMSFileReader.*
+!ext_lib/dotnet/*.dll
+!ext_lib/dotnet/*.xml
+
+# Generated data and test outputs
 neg_esi_srfa_1ppm_test.csv
 neg_esi_srfa_1ppm_test.xlsx
 srfa_results.csv
 srfa_results.json
 example_gcms_results.csv
 example_gcms_results.json
-tests/tests_data/ftms/ESFA_100k_9767-13548_chB.A_re_pc_Averaged1min.h5
 NEG_ESI_SRFA_CoreMS.csv
 NEG_ESI_SRFA_CoreMS.hdf5
 NEG_ESI_SRFA_CoreMS.json
 NEG_ESI_SRFA_CoreMS.xlsx
-random.hdf5
-storage.h5
+NEG_ESI_SRFA_CoreMS_prob_score.csv
+NEG_ESI_SRFA_CoreMS_prob_score.json
 NEG_ESI_SRFA_CoreMS.corems/NEG_ESI_SRFA_CoreMS_scan0.csv
 NEG_ESI_SRFA_CoreMS.corems/NEG_ESI_SRFA_CoreMS_scan0.json
 NEG_ESI_SRFA_CoreMS.corems/NEG_ESI_SRFA_CoreMS_scan0.xlsx
 Chlorophenol Red C19 H12 Cl2 O5 S1.csv
-NEG_ESI_SRFA_CoreMS_prob_score.csv
-NEG_ESI_SRFA_CoreMS_prob_score.json
 test_aggregation.csv
 test.csv
 test.json
+test_LF.csv
+test_LF.png
+test_fig.png
+Loss_finder.csv
+random.hdf5
+storage.h5
 mprofile_*
-tests/tests_data/ftms/20190709_WK_CADY_Auto_S16_H1_Post_O5_1_01_36.txt
+
+# Profiling outputs
 topics.prof
 di-fticr.prof
-.pypirc
 di-fticr.prof.log
 gc-ms.prof
 di-fticr-di.prof
 di-fticr-transient.prof
-test_LF.csv
-test_LF.png
-test_fig.png
-Loss_finder.csv
-results/
-.devcontainer/devcontainer.json
+
+# Databases and large reference inputs
+db/molformula.db
 db/20210203_Peak212_Neg_HR.raw
 db/PNNLMetV20201027.MSL
+
+# Data products
 data/ftms_nom_data_products.json
 data/ftms_nom_metadata_products.json
 data/ftms_nom_nmdc_data.csv
 data/nom_failed_files.json
-db/molformula.db
-.venv/
-clr_test/
-dev/
-r00*/
-!ext_lib/ChemstationMSFileReader.*
-!ext_lib/dotnet/*.dll
-!ext_lib/dotnet/*.xml
-ext_lib/
-*.egg*
-config.yaml
-*.token
+
+# Specific test fixtures
+tests/tests_data/ftms/ESFA_100k_9767-13548_chB.A_re_pc_Averaged1min.h5
+tests/tests_data/ftms/20190709_WK_CADY_Auto_S16_H1_Post_O5_1_01_36.txt
+
+# Dev container overrides
+.devcontainer/devcontainer.json