1.10.2 patch

CHANGELOG.md

@@ -1,8 +1,15 @@
 # nf-core/tools: Changelog
 
+## [v1.10.2 - Copper Camel _(bought back from the dead)_](https://github.com/nf-core/tools/releases/tag/1.10.2) - [2020-07-31]
+
+Second patch release to address some small errors discovered in the pipeline template.
+Apologies for the inconvenience.
+
+* Fix syntax error in `/push_dockerhub.yml` GitHub Action workflow
 * Change `params.readPaths` -> `params.input_paths` in `test_full.config`
+* Check results when posting the lint results as a GitHub comment
 
-## [v1.10.1](https://github.com/nf-core/tools/releases/tag/1.10.1) - [2020-07-30]
+## [v1.10.1 - Copper Camel _(patch)_](https://github.com/nf-core/tools/releases/tag/1.10.1) - [2020-07-30]
 
 Patch release to fix the automatic template synchronisation, which failed in the v1.10 release.
 

docs/lint_errors.md

@@ -177,7 +177,7 @@ This test will fail if the following requirements are not met in these files:
 
 2. `linting.yml`: Specifies the commands to lint the pipeline repository using `nf-core lint` and `markdownlint`
     * Must be turned on for `push` and `pull_request`.
-    * Must have the command `nf-core lint ${GITHUB_WORKSPACE}`.
+    * Must have the command `nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}`.
     * Must have the command `markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml`.
 
 3. `branch.yml`: Ensures that pull requests to the protected `master` branch are coming from the correct branch when a PR is opened against the _nf-core_ repository.

nf_core/lint.py

@@ -771,7 +771,7 @@ def check_actions_lint(self):
                 self.passed.append((5, "Continuous integration runs Markdown lint Tests: `{}`".format(fn)))
 
             # Check that the nf-core linting runs
-            nfcore_lint_cmd = "nf-core lint ${GITHUB_WORKSPACE}"
+            nfcore_lint_cmd = "nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}"
             try:
                 steps = lintwf["jobs"]["nf-core"]["steps"]
                 assert any([nfcore_lint_cmd in step["run"] for step in steps if "run" in step.keys()])
@@ -1440,39 +1440,55 @@ def github_comment(self):
         """
         If we are running in a GitHub PR, try to post results as a comment
         """
-        if os.environ.get("GITHUB_TOKEN", "") != "" and os.environ.get("GITHUB_COMMENTS_URL", "") != "":
-            try:
-                headers = {"Authorization": "token {}".format(os.environ["GITHUB_TOKEN"])}
-                # Get existing comments - GET
-                get_r = requests.get(url=os.environ["GITHUB_COMMENTS_URL"], headers=headers)
-                if get_r.status_code == 200:
-
-                    # Look for an existing comment to update
-                    update_url = False
-                    for comment in get_r.json():
-                        if comment["user"]["login"] == "github-actions[bot]" and comment["body"].startswith(
-                            "\n#### `nf-core lint` overall result"
-                        ):
-                            # Update existing comment - PATCH
-                            log.info("Updating GitHub comment")
-                            update_r = requests.patch(
-                                url=comment["url"],
-                                data=json.dumps({"body": self.get_results_md().replace("Posted", "**Updated**")}),
-                                headers=headers,
-                            )
-                            return
-
-                    # Create new comment - POST
-                    if len(self.warned) > 0 or len(self.failed) > 0:
-                        log.info("Posting GitHub comment")
-                        post_r = requests.post(
-                            url=os.environ["GITHUB_COMMENTS_URL"],
-                            data=json.dumps({"body": self.get_results_md()}),
+        if os.environ.get("GITHUB_TOKEN", "") == "":
+            log.debug("Environment variable GITHUB_TOKEN not found")
+            return
+        if os.environ.get("GITHUB_COMMENTS_URL", "") == "":
+            log.debug("Environment variable GITHUB_COMMENTS_URL not found")
+            return
+        try:
+            headers = {"Authorization": "token {}".format(os.environ["GITHUB_TOKEN"])}
+            # Get existing comments - GET
+            get_r = requests.get(url=os.environ["GITHUB_COMMENTS_URL"], headers=headers)
+            if get_r.status_code == 200:
+
+                # Look for an existing comment to update
+                update_url = False
+                for comment in get_r.json():
+                    if comment["user"]["login"] == "github-actions[bot]" and comment["body"].startswith(
+                        "\n#### `nf-core lint` overall result"
+                    ):
+                        # Update existing comment - PATCH
+                        log.info("Updating GitHub comment")
+                        update_r = requests.patch(
+                            url=comment["url"],
+                            data=json.dumps({"body": self.get_results_md().replace("Posted", "**Updated**")}),
                             headers=headers,
                         )
+                        return
+
+                # Create new comment - POST
+                if len(self.warned) > 0 or len(self.failed) > 0:
+                    r = requests.post(
+                        url=os.environ["GITHUB_COMMENTS_URL"],
+                        data=json.dumps({"body": self.get_results_md()}),
+                        headers=headers,
+                    )
+                    try:
+                        r_json = json.loads(r.content)
+                        response_pp = json.dumps(r_json, indent=4)
+                    except:
+                        r_json = r.content
+                        response_pp = r.content
+
+                    if r.status_code == 201:
+                        log.info("Posted GitHub comment: {}".format(r_json["html_url"]))
+                        log.debug(response_pp)
+                    else:
+                        log.warn("Could not post GitHub comment: '{}'\n{}".format(r.status_code, response_pp))
 
-            except Exception as e:
-                log.warning("Could not post GitHub comment: {}\n{}".format(os.environ["GITHUB_COMMENTS_URL"], e))
+        except Exception as e:
+            log.warning("Could not post GitHub comment: {}\n{}".format(os.environ["GITHUB_COMMENTS_URL"], e))
 
     def _wrap_quotes(self, files):
         if not isinstance(files, list):

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml

@@ -21,7 +21,7 @@ jobs:
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
         # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples) 
+        # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
         {% raw %}env:

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml

@@ -57,5 +57,12 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}
+
+      - name: Upload linting log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: linting-log-file
+          path: lint_log.txt
 {% endraw %}

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub.yml

@@ -8,32 +8,33 @@ on:
   release:
     types: [published]
 
-push_dockerhub:
-  name: Push new Docker image to Docker Hub
-  runs-on: ubuntu-latest
-  # Only run for the nf-core repo, for releases and merged PRs
-  if: {% raw %}${{{% endraw %} github.repository == '{{ cookiecutter.name }}' {% raw %}}}{% endraw %}
-  env:
-    DOCKERHUB_USERNAME: {% raw %}${{ secrets.DOCKERHUB_USERNAME }}{% endraw %}
-    DOCKERHUB_PASS: {% raw %}${{ secrets.DOCKERHUB_PASS }}{% endraw %}
-  steps:
-    - name: Check out pipeline code
-      uses: actions/checkout@v2
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: {% raw %}${{{% endraw %} github.repository == '{{ cookiecutter.name }}' {% raw %}}}{% endraw %}
+    env:
+      DOCKERHUB_USERNAME: {% raw %}${{ secrets.DOCKERHUB_USERNAME }}{% endraw %}
+      DOCKERHUB_PASS: {% raw %}${{ secrets.DOCKERHUB_PASS }}{% endraw %}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
 
-    - name: Build new docker image
-      run: docker build --no-cache . -t {{ cookiecutter.name_docker }}:latest
+      - name: Build new docker image
+        run: docker build --no-cache . -t {{ cookiecutter.name_docker }}:latest
 
-    - name: Push Docker image to DockerHub (dev)
-      if: {% raw %}${{ github.event_name == 'push' }}{% endraw %}
-      run: |
-        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-        docker tag {{ cookiecutter.name_docker }}:latest {{ cookiecutter.name_docker }}:dev
-        docker push {{ cookiecutter.name_docker }}:dev
+      - name: Push Docker image to DockerHub (dev)
+        if: {% raw %}${{ github.event_name == 'push' }}{% endraw %}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker tag {{ cookiecutter.name_docker }}:latest {{ cookiecutter.name_docker }}:dev
+          docker push {{ cookiecutter.name_docker }}:dev
 
-    - name: Push Docker image to DockerHub (release)
-      if: {% raw %}${{ github.event_name == 'release' }}{% endraw %}
-      run: |
-        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-        docker push {{ cookiecutter.name_docker }}:latest
-        docker tag {{ cookiecutter.name_docker }}:latest {{ cookiecutter.name_docker }}:{% raw %}${{ github.event.release.tag_name }}{% endraw %}
-        docker push {{ cookiecutter.name_docker }}:{% raw %}${{ github.event.release.tag_name }}{% endraw %}
+      - name: Push Docker image to DockerHub (release)
+        if: {% raw %}${{ github.event_name == 'release' }}{% endraw %}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push {{ cookiecutter.name_docker }}:latest
+          docker tag {{ cookiecutter.name_docker }}:latest {{ cookiecutter.name_docker }}:{% raw %}${{ github.event.release.tag_name }}{% endraw %}
+          docker push {{ cookiecutter.name_docker }}:{% raw %}${{ github.event.release.tag_name }}{% endraw %}

nf_core/sync.py

@@ -79,12 +79,11 @@ def sync(self):
         """ Find workflow attributes, create a new template pipeline on TEMPLATE
         """
 
-        config_log_msg = "Pipeline directory: {}".format(self.pipeline_dir)
+        log.debug("Pipeline directory: {}".format(self.pipeline_dir))
         if self.from_branch:
-            config_log_msg += "\n  Using branch `{}` to fetch workflow variables".format(self.from_branch)
+            log.debug("Using branch `{}` to fetch workflow variables".format(self.from_branch))
         if self.make_pr:
-            config_log_msg += "\n  Will attempt to automatically create a pull request on GitHub.com"
-        log.info(config_log_msg)
+            log.debug("Will attempt to automatically create a pull request")
 
         self.inspect_sync_dir()
         self.get_wf_config()
@@ -388,11 +387,7 @@ def sync_all_pipelines(gh_username=None, gh_auth_token=None):
             log.error("Something went wrong when syncing {}:\n{}".format(wf.full_name, e))
             failed_syncs.append(wf.name)
         else:
-            log.info(
-                "[green]Sync successful for {0}:[/] [blue][link={1}]{1}[/link]".format(
-                    wf.full_name, sync_obj.gh_pr_returned_data.get("html_url")
-                )
-            )
+            log.info("[green]Sync successful for {}".format(wf.full_name))
             successful_syncs.append(wf.name)
 
         # Clean up

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 import sys
 
-version = "1.10.1"
+version = "1.10.2"
 
 with open("README.md") as f:
     readme = f.read()

tests/lint_examples/minimalworkingexample/.github/workflows/linting.yml

@@ -41,5 +41,4 @@ jobs:
         run: |
           pip install nf-core
       - name: Run nf-core lint
-        run: |
-          nf-core lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}