Move calculation and plot methods (#17)

* history, test fixes * refactor history, introduce ExecutedStep dataclass * start using history in run, think about CLI * add max_quant_import * expand CLI example * add History.pop_step, disk_memory mode * added back function to run * moved "small plots" to protzilla2 and created single methods for each plot type * initial exploration of integration plots into data preprocessing * add docstrings for history * separated calculation and plots in data preprocessing * added create_plot and create_plot_from_location to Run class * black * small changes and fix test protein filter * moved normalisation methods and tests test for reference protein normalisation is not working * fixed normalisation tests * added group_by parameter in normalisation * renamed fixtures * moved test_plotting to test_run and renamed it to test_run_calculate_from_location * fixed some merge conflicts * added docstring to migrated methds * add docstring to filter proteins and minor changes * reformatting * Update protzilla/constants/method_mapping.py Co-authored-by: antonneubauer <[email protected]> * renamed method_mapping to location_mapping and added short description for data structures * Update protzilla/data_preprocessing/normalisation.py Co-authored-by: antonneubauer <[email protected]> * Update protzilla/data_preprocessing/plots.py Co-authored-by: antonneubauer <[email protected]> * Update protzilla/data_preprocessing/plots.py Co-authored-by: antonneubauer <[email protected]> * added conftest with option show-figures * added show_figure to test_filter_proteins and renamed fixture * normalisation plot methods return now a list * added z_score normalisation * small changes in docstring from normalisation and filter proteins * added log_transformation * added outlier detection methds * added outlier detection plots * added tests for filter_samples * added filter_samples plot * added knn imputation * added all imputation methods * fixed tests, added plot tests for imputation * starting test_plots, not finished * adding test_plots and fixing pytest_dependencies * merge from main * Apply suggestions from code review Co-authored-by: antonneubauer <[email protected]> * adopting changes * reformatted with black * reformat with precommithook * remove comment --------- Co-authored-by: brokkoli71 <[email protected]> Co-authored-by: Fynn <[email protected]> Co-authored-by: antonneubauer <[email protected]> Co-authored-by: brokkoli71 <[email protected]>
cschlaffner · Mar 16, 2023 · 148ba0e · 148ba0e
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diff --git a/.coveragerc b/.coveragerc
@@ -1,3 +1,3 @@
-[coverage:run]
-relative_files = True
-omit = user_data/*, db.sqlite3, constants/*, 
+[coverage:run]
+relative_files = True
+omit = user_data/*, db.sqlite3, constants/*, 
diff --git a/.github/ISSUE_TEMPLATE/issue.md b/.github/ISSUE_TEMPLATE/issue.md
@@ -1,15 +1,15 @@
----
-name: Issue Template
-about: Standard Issue Template
-title: 
-labels: 
-project: PROTzilla 2
-
----
-
-<Useful Description>
-
-
-
-## Acceptance Criteria
-- [ ] 
+---
+name: Issue Template
+about: Standard Issue Template
+title: 
+labels: 
+project: PROTzilla 2
+
+---
+
+<Useful Description>
+
+
+
+## Acceptance Criteria
+- [ ] 
diff --git a/.github/ISSUE_TEMPLATE/todo_issue.md b/.github/ISSUE_TEMPLATE/todo_issue.md
@@ -1,12 +1,12 @@
----
-name: TODO Template
-about: TODO Issue Template
-title: '#TODO <issue_nr>'
-labels: todo
-project: 'PROTzilla2'
-
----
-
-<Description>
-
-search for #TODO <issue_nr>
+---
+name: TODO Template
+about: TODO Issue Template
+title: '#TODO <issue_nr>'
+labels: todo
+project: 'PROTzilla2'
+
+---
+
+<Description>
+
+search for #TODO <issue_nr>
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,11 +1,11 @@
-PR for #<Issue Number>
-
-Description (what might a Reviewer want to know)
-
-## PR checklist
-
-- [ ] main-branch has been merged into local branch to resolve conflicts
-- [ ] tests and linter have passed AFTER local merge
-- [ ] at least one other dev reviewed and approved
-- [ ] documentation
-- [ ] tests
+PR for #<Issue Number>
+
+Description (what might a Reviewer want to know)
+
+## PR checklist
+
+- [ ] main-branch has been merged into local branch to resolve conflicts
+- [ ] tests and linter have passed AFTER local merge
+- [ ] at least one other dev reviewed and approved
+- [ ] documentation
+- [ ] tests
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,48 +1,48 @@
-name: CI Pipeline
-on:
-  pull_request:
-    branches:
-      - '*'
-  push:
-    branches:
-      - main
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/[email protected]
-      - name: Setup Python
-        uses: actions/[email protected]
-        with:
-          python-version: "3.11"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest pytest-cov
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      
-      - name: Analysing the code with autoflake
-        run: python -m autoflake --in-place --remove-all-unused-imports --remove-unused-variables --expand-star-imports --ignore-init-module-imports $(git ls-files '*.py')
-
-      - name: run tests, build coverage file
-        run: |
-          export PYTHONPATH=. pytest
-          pytest --cache-clear --cov=. --cov-branch --cov-report term-missing tests/protzilla
-      
-      - name: format with black
-        run: python -m black .
-
-      - name: Coverage comment
-        id: coverage_comment
-        uses: py-cov-action/python-coverage-comment-action@v3
-        with:
-          GITHUB_TOKEN: ${{ github.token }}
-
-      - name: Store Pull Request comment to be posted
-        uses: actions/upload-artifact@v3
-        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
-        with:
-          name: python-coverage-comment-action
-          path: python-coverage-comment-action.txt
+name: CI Pipeline
+on:
+  pull_request:
+    branches:
+      - '*'
+  push:
+    branches:
+      - main
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+      - name: Setup Python
+        uses: actions/[email protected]
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest pytest-cov
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      
+      - name: Analysing the code with autoflake
+        run: python -m autoflake --in-place --remove-all-unused-imports --remove-unused-variables --expand-star-imports --ignore-init-module-imports $(git ls-files '*.py')
+
+      - name: run tests, build coverage file
+        run: |
+          export PYTHONPATH=. pytest
+          pytest --cache-clear --cov=. --cov-branch --cov-report term-missing tests/protzilla
+      
+      - name: format with black
+        run: python -m black .
+
+      - name: Coverage comment
+        id: coverage_comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+
+      - name: Store Pull Request comment to be posted
+        uses: actions/upload-artifact@v3
+        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
+        with:
+          name: python-coverage-comment-action
+          path: python-coverage-comment-action.txt
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -1,24 +1,24 @@
-name: Post coverage comment
-
-on:
-  workflow_run:
-    workflows: ["CI"]
-    types:
-      - completed
-
-jobs:
-  test:
-    name: Run tests & display coverage
-    runs-on: ubuntu-latest
-    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
-    steps:
-      # DO NOT run actions/checkout@v2 here, for security reasons
-      # For details, refer to https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
-      - name: Post comment
-        uses: py-cov-action/python-coverage-comment-action@v3
-        with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}
-          # Update those if you changed the default values:
-          # COMMENT_ARTIFACT_NAME: python-coverage-comment-action
-          # COMMENT_FILENAME: python-coverage-comment-action.txt
+name: Post coverage comment
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types:
+      - completed
+
+jobs:
+  test:
+    name: Run tests & display coverage
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    steps:
+      # DO NOT run actions/checkout@v2 here, for security reasons
+      # For details, refer to https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+      - name: Post comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}
+          # Update those if you changed the default values:
+          # COMMENT_ARTIFACT_NAME: python-coverage-comment-action
+          # COMMENT_FILENAME: python-coverage-comment-action.txt