Merge branch 'master' into ns-rse/259-muropeptides-wasm-working

Mesnage-Org · Jun 4, 2024 · c4b6591 · c4b6591
2 parents 7b84a44 + 1500505
commit c4b6591
Show file tree

Hide file tree

Showing 9 changed files with 1,090 additions and 1,076 deletions.
diff --git a/.github/workflows/lib-tests.yml b/.github/workflows/lib-tests.yml
@@ -10,9 +10,10 @@ jobs:
     name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
     defaults:
       run:
         working-directory: ./lib

diff --git a/.github/workflows/release-to-pypi.yml b/.github/workflows/release-to-pypi.yml
@@ -20,7 +20,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4.3.0
         with:
-          python-version: 3.9
+          python-version: "3.11"
       - name: Installing the package
         run: |
           pip3 install .

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.2.0] - 2024-03-20
+
+### Added
+
+- Added automatic structure consolidation for single datasets (#266)
+- Parameterized column names via `config/columns.yaml` (#269 + #275)
+
+### Changed
+
+- Bumped minimum Python version to 3.10 (#269)
+- Renamed old columns with `(consolidated)` to `(best match)` (#269)
+
 ## [1.1.1] - 2023-11-06
 
 ### Changed
@@ -64,7 +76,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Let there be peptidoglycan.
 
-[Unreleased]: https://github.com/Mesnage-Org/pgfinder/compare/v1.1.1...HEAD
+[Unreleased]: https://github.com/Mesnage-Org/pgfinder/compare/v1.2.0...HEAD
+[1.2.0]: https://github.com/Mesnage-Org/pgfinder/compare/v1.1.1...v1.2.0
 [1.1.1]: https://github.com/Mesnage-Org/pgfinder/compare/v1.1.0...v1.1.1
 [1.1.0]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.3...v1.1.0
 [1.0.3]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.2...v1.0.3

diff --git a/lib/pgfinder/matching.py b/lib/pgfinder/matching.py
@@ -582,7 +582,7 @@ def pick_from_highest_intensity_instance(column: pd.Series):
         .reset_index()
     )
     total_intensity = consolidated_df[intensity_column].sum()
-    consolidated_df[abundance_column] = consolidated_df[intensity_column] / total_intensity
+    consolidated_df[abundance_column] = consolidated_df[intensity_column] / total_intensity * 100
 
     consolidated_df[oligomer_column] = consolidated_df[structure_column].apply(lambda s: s[-1])
     consolidated_df.sort_values(
@@ -594,7 +594,6 @@ def pick_from_highest_intensity_instance(column: pd.Series):
         [total_column, structure_column, abundance_column, rt_column, theo_column, ppm_column]
     ]
 
-    consolidated_df[abundance_column] = consolidated_df[abundance_column].round(4)
     consolidated_df[rt_column] = consolidated_df[rt_column].round(2)
     consolidated_df[ppm_column] = consolidated_df[ppm_column].round(1)
     # Rename columns using mapping defined in pgfinder/config/columns.yaml under 'consolidation'

diff --git a/...regtest_outputs/test_regression.test_matching_ftrs_baseline[ftrs_test_data_3.11.ftrs].out b/...regtest_outputs/test_regression.test_matching_ftrs_baseline[ftrs_test_data_3.11.ftrs].out
diff --git a/..._regtest_outputs/test_regression.test_matching_ftrs_baseline[ftrs_test_data_5.2.ftrs].out b/..._regtest_outputs/test_regression.test_matching_ftrs_baseline[ftrs_test_data_5.2.ftrs].out
diff --git a/lib/tests/_regtest_outputs/test_regression.test_matching_mq_baseline.out b/lib/tests/_regtest_outputs/test_regression.test_matching_mq_baseline.out
diff --git a/lib/tests/resources/consolidated.csv b/lib/tests/resources/consolidated.csv
@@ -1,7 +1,7 @@
 RT (min),Theo (Da),Delta (ppm),Inferred structure (best match),Intensity (best match),Total Intensity,Structure,Abundance (%),Consolidated RT (min),Consolidated Theo (Da),Consolidated Delta (ppm)
-1,100,0.1,gm|0,100,360,gm|0,0.5278,1,100,0.1
-2,200,0.2,"gm-AEJN|1,   gm-AEJGG|1,   gm-AEJX|1",50,,"gm-AEJN|1,   gm-AEJGG|1,   gm-AEJX|1",0.4167,4,400,0.4
-3,300,0.3,gm-AEJR|1,20,,gm-AEJR|1,0.0556,3,300,0.3
+1,100,0.1,gm|0,100,360,gm|0,52.7777777777778,1,100,0.1
+2,200,0.2,"gm-AEJN|1,   gm-AEJGG|1,   gm-AEJX|1",50,,"gm-AEJN|1,   gm-AEJGG|1,   gm-AEJX|1",41.6666666666667,4,400,0.4
+3,300,0.3,gm-AEJR|1,20,,gm-AEJR|1,5.55555555555556,3,300,0.3
 4,400,0.4,"gm-AEJN|1,   gm-AEJGG|1,   gm-AEJX|1",60,,,,,,
 5,500,0.5,gm|0,90,,,,,,
 6,600,0.6,"gm-AEJN|1,   gm-AEJGG|1,   gm-AEJX|1",40,,,,,,
diff --git a/web/playwright.config.ts b/web/playwright.config.ts
@@ -6,7 +6,8 @@ const config: PlaywrightTestConfig = {
 		port: 4173
 	},
 	testDir: 'tests',
-	testMatch: /(.+\.)?(test|spec)\.[jt]s/
+	testMatch: /(.+\.)?(test|spec)\.[jt]s/,
+	timeout: 5 * 60 * 1000
 };
 
 export default config;