Merge pull request #23 from SchlossLab/gh-actions

Fix GitHub Actions workflows

Author: kelly-sovacool

.github/workflows/build.yml

@@ -8,45 +8,45 @@ on:
 jobs:
   build:
     name: build
-    runs-on: macOS-latest
+    runs-on: macos-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           persist-credentials: false
           fetch-depth: 0
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@v1
-      - uses: actions/setup-python@v1
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install build dependencies
+      - name: git config
         run: |
-          Rscript -e "install.packages(c('styler','usethis'))"
-          python -m pip install --upgrade pip
-          pip install black snakefmt
+          git config --local user.email "noreply@github.com"
+          git config --local user.name "GitHub"
       - name: Style R code
         run: |
+          Rscript -e "install.packages(c('styler','usethis'))"
           Rscript -e 'usethis::use_tidy_style()'
           git add .
           git diff-index --quiet HEAD \
           || git commit \
-          --author="github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>" \
           -m '🎨  Style R code'
       - name: Style Python code
         run: |
+          python -m pip install --upgrade pip
+          pip install black snakefmt
           black workflow/
           snakefmt workflow/
           git add workflow/
           git diff-index --quiet HEAD \
           || git commit \
-          --author="github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>" \
           -m '🎨  Style Python & Snakemake code 🐍'
       - name: Push
         uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: ${{ github.head_ref }}
+          branch: ${{ github.head_ref }}

.github/workflows/release-please.yml

@@ -2,53 +2,44 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - main
   pull_request:
-    branches: [ main ]
-
+    branches:
+      - main
 
 jobs:
-  # Formatting:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v2
-  #     - name: Formatting
-  #       uses: github/super-linter@v4
-  #       env:
-  #         VALIDATE_ALL_CODEBASE: false
-  #         DEFAULT_BRANCH: main
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  #         VALIDATE_SNAKEMAKE_SNAKEFMT: true
-
-  Linting:
+  tests:
+    name: tests
     runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .
-        snakefile: workflow/Snakefile
-        args: "--lint"
+    strategy:
+      matrix:
+        python-version: ["3.11"]
 
-#  Testing:
-#    runs-on: ubuntu-latest
-#    needs:
-#      - Linting
-#      - Formatting
-#    steps:
-#    - uses: actions/checkout@v2
-
-#    - name: Test workflow
-#      uses: snakemake/snakemake-github-action@v1.24.0
-#      with:
-#        directory: .test
-#        snakefile: workflow/Snakefile
-#        args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp --configfile config/test.yml"
-
-#    - name: Test report
-#      uses: snakemake/snakemake-github-action@v1.24.0
-#      with:
-#        directory: .test
-#        snakefile: workflow/Snakefile
-#        args: "--report report.zip"
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-parallel
+      - name: Lint workflow
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: .
+          snakefile: workflow/Snakefile
+          args: "--lint"
+      - name: Run test workflow
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: .
+          snakefile: workflow/Snakefile
+          args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --all-temp --conda-frontend mamba --configfile config/test.yml"
+#      - name: Test with pytest
+#        run: |
+#          pytest --workers 2 .tests/

.github/workflows/tests.yml

@@ -2,8 +2,10 @@
 data/
 log/
 benchmarks/
-results/
+results/*/runs
 .Rproj.user
 *KLS*
 *_test*
-.vscode/
+.vscode/
+!.tests/
+__pycache__/

.gitignore

@@ -0,0 +1,17 @@
+# pytest status
+
+| unit test file               | status |
+|------------------------------|--------|
+| test_combine_benchmarks      | ✅     |
+| test_combine_hp_performance  | ❌     |
+| test_combine_results         | ✅     |
+| test_find_feature_importance | ✅     |
+| test_plot_benchmarks         | ❌     |
+| test_plot_feature_importance | ❌     |
+| test_plot_hp_performance     | ✅     |
+| test_plot_performance        | ❌     |
+| test_preprocess_data         | ❌     |
+| test_render_report           | ❌     |
+| test_run_ml                  | ❌     |
+
+Need to change how some results files are compared instead of byte-by-byte.

.tests/unit/README.md

@@ -0,0 +1,2 @@
+s	h:m:s	max_rss	max_vms	max_uss	max_pss	io_in	io_out	mean_load	cpu_time
+9.3403	0:00:09	0	0	0	0	0.00	0.00	191.90	0

.tests/unit/combine_benchmarks/data/benchmarks/otu-mini-bin/runs/run_ml.glmnet_100.txt

@@ -0,0 +1,2 @@
+s	h:m:s	max_rss	max_vms	max_uss	max_pss	io_in	io_out	mean_load	cpu_time
+9.5682	0:00:09	0	0	0	0	0.00	0.00	209.26	0

.tests/unit/combine_benchmarks/data/benchmarks/otu-mini-bin/runs/run_ml.glmnet_101.txt

@@ -0,0 +1,16 @@
+schtools::log_snakemake()
+library(tidyverse)
+
+read_bench <- function(filename) {
+  read_tsv(filename) %>%
+    mutate(
+      method = str_replace(filename, "^benchmarks/(.*)/runs/run_ml.(.*)_(.*).txt", "\\2"),
+      seed = str_replace(filename, "^benchmarks/(.*)/runs/run_ml.(.*)_(.*).txt", "\\3")
+    )
+}
+
+dat <- snakemake@input[["tsv"]] %>%
+  lapply(read_bench) %>%
+  bind_rows()
+head(dat)
+write_csv(dat, snakemake@output[["csv"]])

.tests/unit/combine_benchmarks/data/workflow/scripts/combine_benchmarks.R

@@ -0,0 +1,3 @@
+s,h:m:s,max_rss,max_vms,max_uss,max_pss,io_in,io_out,mean_load,cpu_time,method,seed
+9.3403,00:00:09,0,0,0,0,0,0,191.9,0,glmnet,100
+9.5682,00:00:09,0,0,0,0,0,0,209.26,0,glmnet,101