Merge branch 'main' of https://github.com/savitakartik/tsinfer-qc

.github/workflows/post.yml

@@ -0,0 +1,108 @@
+name: Post screenshots
+
+on:
+  pull_request_target:
+
+jobs:
+  post:
+    name: Python
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    env:
+      SCREENSHOTS_BRANCH: "pr-screenshots"
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install deps
+        run: pip install -r requirements.txt
+
+      - name: Create Screenshots
+        run: |
+          msp simulate --length 1000 --recombination-rate 0.01 --mutation-rate 0.01 100 out.trees
+          python -m tsbrowse preprocess out.trees
+          python -m tsbrowse screenshot out.tsbrowse mutations
+          python -m tsbrowse screenshot out.tsbrowse edges
+          python -m tsbrowse screenshot out.tsbrowse nodes
+
+      - name: Commit Screenshots
+        run: |
+          git config --global user.name 'GitHub Action'
+          git config --global user.email '[email protected]'
+          pr_number="${{ github.event.pull_request.number }}"
+          screenshot_dir="pr_${pr_number}"
+          
+          if ! git ls-remote --exit-code --heads origin $SCREENSHOTS_BRANCH; then
+            git checkout --orphan $SCREENSHOTS_BRANCH
+            git rm -rf .
+            git commit --allow-empty -m "Initial commit for screenshots branch"
+            git push origin $SCREENSHOTS_BRANCH
+          else
+            git fetch origin $SCREENSHOTS_BRANCH
+            git checkout $SCREENSHOTS_BRANCH
+          fi
+          
+          mkdir -p $screenshot_dir
+          mv *.png $screenshot_dir/
+          
+          git add $screenshot_dir
+          git commit -m "Update screenshots for PR #${pr_number}"
+          git push origin $SCREENSHOTS_BRANCH
+
+      - name: Update or Post Comment
+        uses: actions/github-script@v6
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const fs = require('fs').promises;
+            
+            const prNumber = context.payload.pull_request.number;
+            const screenshotDir = `pr_${prNumber}`;
+            const pngFiles = (await fs.readdir(screenshotDir)).filter(file => file.endsWith('.png'));
+            
+            let commentBody = '## Automated Screenshots\n\n';
+            commentBody += 'These screenshots are automatically updated as the PR changes.\n\n';
+            commentBody += '<details><summary>Click to view screenshots</summary>\n\n';
+            for (const file of pngFiles) {
+              const imageUrl = `https://raw.githubusercontent.com/${context.repo.owner}/${context.repo.repo}/${process.env.SCREENSHOTS_BRANCH}/${screenshotDir}/${file}`;
+              commentBody += `### ${file}\n\n![${file}](${imageUrl})\n\n`;
+            }
+            commentBody += '</details>';
+            
+            const { data: comments } = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: prNumber,
+            });
+            
+            const botComment = comments.find(comment => 
+              comment.user.type === 'Bot' && comment.body.includes('## Automated Screenshots')
+            );
+            
+            if (botComment) {
+              await github.rest.issues.updateComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                comment_id: botComment.id,
+                body: commentBody,
+              });
+              console.log('Updated existing comment');
+            } else {
+              await github.rest.issues.createComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: prNumber,
+                body: commentBody,
+              });
+              console.log('Created new comment');
+            }

.github/workflows/tests.yml

@@ -33,7 +33,7 @@ jobs:
         shell: bash
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.10.0
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           access_token: ${{ github.token }}
 
@@ -50,7 +50,7 @@ jobs:
 
       - name: Tests with numba
         run: coverage run --source=tsbrowse -m pytest -x tests
-    
+
       - name: Tests with coverage (no numba)
         run: TSBROWSE_DISABLE_NUMBA=1 coverage run --source=tsbrowse -m pytest -x tests
 

README.md

@@ -8,13 +8,23 @@ It is particularly useful to help evaluate ARGs that have been inferred using to
 [KwARG](https://github.com/a-ignatieva/kwarg),
 [Threads](https://pypi.org/project/threads-arg/), etc.
 
+To view a tskit tree sequence or tszip file first pre-process it:
+
+`python -m tsbrowse preprocess /path/to/trees-file`
+
+This will write a `.tsbrowse` file
+
 To launch the app use:
 
-`python -m tsbrowse /path/to/trees-file`
+`python -m tsbrowse serve /path/to/tsbrowse-file`
+
+Or to generate a PNG of a specific page use, e.g:
+
+`python -m tsbrowse screenshot /path/to/tsbrowse-file mutations`
 
 On WSL, it may be necessary to disable Numba's CUDA support:
 
-`NUMBA_DISABLE_CUDA=1 python -m tsbrowse /path/to/trees-file`
+`NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file`
 
 ## Installation
 

tests/test_cli.py

@@ -0,0 +1,70 @@
+import os
+
+import tszip
+from click.testing import CliRunner
+from PIL import Image
+
+from . import test_preprocess
+from tsbrowse import __main__ as main
+
+
+def test_preprocess_cli(tmpdir):
+    tszip_path = os.path.join(tmpdir, "test_input.tszip")
+    default_output_path = os.path.join(tmpdir, "test_input.tsbrowse")
+    custom_output_path = os.path.join(tmpdir, "custom_input.tsbrowse")
+
+    ts = test_preprocess.single_tree_example_ts()
+    tszip.compress(ts, tszip_path)
+
+    runner = CliRunner()
+    result = runner.invoke(main.cli, ["preprocess", tszip_path])
+    assert result.exit_code == 0
+    assert os.path.exists(default_output_path)
+    tszip.load(default_output_path).tables.assert_equals(ts.tables)
+
+    result = runner.invoke(
+        main.cli, ["preprocess", tszip_path, "--output", custom_output_path]
+    )
+    assert result.exit_code == 0
+    assert os.path.exists(custom_output_path)
+    tszip.load(custom_output_path).tables.assert_equals(ts.tables)
+
+
+def test_screenshot_cli(tmpdir):
+    tszip_path = os.path.join(tmpdir, "test_input.tszip")
+    tsbrowse_path = os.path.join(tmpdir, "test_input.tsbrowse")
+    ts = test_preprocess.single_tree_example_ts()
+    tszip.compress(ts, tszip_path)
+    runner = CliRunner()
+    result = runner.invoke(main.cli, ["preprocess", tszip_path])
+    assert result.exit_code == 0
+
+    # Test with default output
+    result = runner.invoke(main.cli, ["screenshot", tsbrowse_path, "overview"])
+    assert result.exit_code == 0
+    default_output = os.path.join(tmpdir, "test_input_overview.png")
+    assert os.path.exists(default_output)
+    with Image.open(default_output) as img:
+        width, height = img.size
+        assert width == 1560
+        assert height == 296
+
+    # Test with path
+    custom_output = os.path.join(tmpdir, "custom_screenshot.png")
+    result = runner.invoke(
+        main.cli,
+        [
+            "screenshot",
+            tsbrowse_path,
+            "overview",
+            "--output",
+            custom_output,
+        ],
+    )
+    assert result.exit_code == 0
+    assert os.path.exists(custom_output)
+
+    # Test with invalid page
+    result = runner.invoke(main.cli, ["screenshot", tsbrowse_path, "InvalidPage"])
+    assert result.exit_code != 0
+    assert "Invalid value" in result.output