Merge pull request #784 from nf-core/dev

v1.12 dev -> master

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,45 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
+<!--
+# nf-core/tools bug report
+
+Hi there!
+
+Thanks for telling us about a problem with the nf-core/tools package.
+Please delete this text and anything that's not relevant from the template below:
+-->
+
+## Description of the bug
+
+<!-- A clear and concise description of what the bug is. -->
+
+## Steps to reproduce
+
+Steps to reproduce the behaviour:
+
+1. Command line: <!-- [e.g. `nf-core lint ...`] -->
+2. See error: <!-- [Please provide your error message] -->
+
+## Expected behaviour
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## System
+
+- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
+- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
+- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
+- Version of nf-core/tools: <!-- [e.g. 1.1, 1.5, 1.8.2...] -->
+- Python version: <!-- [e.g. 3.7, 3.8...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #tools channel"
+    url: https://nfcore.slack.com/channels/tools
+    about: Discussion about the nf-core/tools package

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core website
+labels: enhancement
+---
+
+<!--
+# nf-core/tools feature request
+
+Hi there!
+
+Thanks for suggesting a new feature for the nf-core/tools package!
+Please delete this text and anything that's not relevant from the template below:
+-->
+
+## Is your feature request related to a problem? Please describe
+
+<!-- A clear and concise description of what the problem is. -->
+
+<!-- e.g. [I'm always frustrated when ...] -->
+
+## Describe the solution you'd like
+
+<!-- A clear and concise description of what you want to happen. -->
+
+## Describe alternatives you've considered
+
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+## Additional context
+
+<!-- Add any other context about the feature request here. -->

.github/workflows/branch.yml

@@ -2,14 +2,13 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
+  pull_request_target:
     branches: [master]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/tools'

.github/workflows/create-lint-wf.yml

@@ -19,6 +19,8 @@ jobs:
           pip install .
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           mkdir /tmp/nextflow
           cd /tmp/nextflow

.github/workflows/pytest.yml

@@ -32,6 +32,8 @@ jobs:
         pip install -e .
 
     - name: Install Nextflow
+      env:
+          CAPSULE_LOG: none
       run: |
         mkdir /tmp/nextflow
         cd /tmp/nextflow

.github/workflows/sync.yml

@@ -45,6 +45,8 @@ jobs:
           pip install .
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           mkdir /tmp/nextflow
           cd /tmp/nextflow

CHANGELOG.md

@@ -1,5 +1,30 @@
 # nf-core/tools: Changelog
 
+## [v1.12 - Mercury Weasel](https://github.com/nf-core/tools/releases/tag/1.12) - [2020-11-19]
+
+### Tools helper code
+
+* Updated `nf_core` documentation generator for building [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
+
+### Template
+
+* Make CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]
+  * Branch protection and linting results should now show on all PRs
+* Updated GitHub issue templates, which had stopped working
+* Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
+  * DockerHub push workflow split into two - one for dev, one for releases
+* Updated actions to no longer use `set-env` which is now depreciating [[#739](https://github.com/nf-core/tools/issues/739)]
+* Added config import for `test_full` in `nextflow.config`
+* Switched depreciated `$baseDir` to `$projectDir`
+* Updated minimum Nextflow version to `20.04.10`
+* Make Nextflow installation less verbose in GitHub Actions [[#780](https://github.com/nf-core/tools/pull/780)]
+
+### Linting
+
+* Updated code to display colours in GitHub Actions log output
+* Allow tests to pass with `dev` version of nf-core/tools (previous failure due to base image version)
+* Lint code no longer tries to post GitHub PR comments. This is now done in a GitHub Action only.
+
 ## [v1.11 - Iron Tiger](https://github.com/nf-core/tools/releases/tag/1.11) - [2020-10-27]
 
 ### Template

README.md

@@ -478,8 +478,8 @@ $ nf-core lint .
 │ [!] 3 Test Warnings                                                                                      │
 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────┤
 │ https://nf-co.re/errors#5: GitHub Actions AWS full test should test full datasets: nf-core-testpipeline… │
-│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::fastqc=0.11.8, 0.11.9 avail… │
-│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::multiqc=1.7, 1.9 available   │
+│ https://nf-co.re/errors#8: Conda dep outdated: bioconda::fastqc=0.11.8, 0.11.9 available                 │
+│ https://nf-co.re/errors#8: Conda dep outdated: bioconda::multiqc=1.7, 1.9 available                      │
 ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ╭───────────────────────╮
 │ LINT RESULTS SUMMARY  │

docs/api/_src/bump_version.rst

@@ -2,4 +2,7 @@ nf_core.bump_version
 ====================
 
 .. automodule:: nf_core.bump_version
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/conf.py

@@ -14,6 +14,7 @@
 #
 import os
 import sys
+import nf_core
 
 sys.path.insert(0, os.path.abspath("../../../nf_core"))
 
@@ -24,9 +25,9 @@
 author = "Phil Ewels, Sven Fillinger"
 
 # The short X.Y version
-version = "1.4"
+version = nf_core.__version__
 # The full version, including alpha/beta/rc tags
-release = "1.4"
+release = nf_core.__version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -65,7 +66,7 @@
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = None
+# pygments_style = None
 
 
 # -- Options for HTML output -------------------------------------------------

docs/api/_src/create.rst

@@ -2,4 +2,7 @@ nf_core.create
 ==============
 
 .. automodule:: nf_core.create
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/download.rst

@@ -2,4 +2,7 @@ nf_core.download
 ================
 
 .. automodule:: nf_core.download
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/index.rst

@@ -9,15 +9,9 @@ Welcome to nf-core tools API documentation!
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
+   :glob:
 
-   bump_version
-   create
-   download
-   licences
-   lint
-   list
-   utils
-   workflow
+   *
 
 
 Indices and tables

docs/api/_src/launch.rst

@@ -0,0 +1,8 @@
+nf_core.launch
+============
+
+.. automodule:: nf_core.launch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/licences.rst

@@ -2,4 +2,7 @@ nf_core.licences
 ================
 
 .. automodule:: nf_core.licences
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/lint.rst

@@ -2,4 +2,7 @@ nf_core.lint
 ============
 
 .. automodule:: nf_core.lint
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/list.rst

@@ -2,4 +2,7 @@ nf_core.list
 ============
 
 .. automodule:: nf_core.list
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/modules.rst

@@ -0,0 +1,8 @@
+nf_core.modules
+============
+
+.. automodule:: nf_core.modules
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/schema.rst

@@ -0,0 +1,8 @@
+nf_core.schema
+============
+
+.. automodule:: nf_core.schema
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/sync.rst

@@ -0,0 +1,8 @@
+nf_core.sync
+==============
+
+.. automodule:: nf_core.sync
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/api/_src/utils.rst

@@ -2,4 +2,7 @@ nf_core.utils
 =============
 
 .. automodule:: nf_core.utils
-    :members:
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/lint_errors.md

@@ -47,6 +47,8 @@ The following files will cause a failure if the _are_ present (to fix, delete th
     deleted and new `nextflow_schema.json` files created instead.
 * `bin/markdown_to_html.r`
   * The old markdown to HTML conversion script, now replaced by `markdown_to_html.py`
+* `.github/workflows/push_dockerhub.yml`
+  * The old dockerhub build script, now split into `.github/workflows/push_dockerhub_dev.yml` and `.github/workflows/push_dockerhub_release.yml`
 
 ## Error #2 - Docker file check failed ## {#2}
 
@@ -238,13 +240,14 @@ You can trigger the tests by going to the `Actions` tab on the pipeline GitHub r
 Additionally, we provide the possibility of testing the pipeline on full size datasets on AWS.
 This should ensure that the pipeline runs as expected on AWS and provide a resource estimation.
 The GitHub Actions workflow is `awsfulltest.yml`, and it can be found in the `.github/workflows/` directory.
-This workflow incurrs higher AWS costs, therefore it should only be triggered on `release` and `workflow_dispatch`.
+This workflow incurrs higher AWS costs, therefore it should only be triggered for releases (`workflow_run` - after the docker hub release workflow) and `workflow_dispatch`.
 You can trigger the tests by going to the `Actions` tab on the pipeline GitHub repository and selecting the `nf-core AWS full size tests` workflow on the left.
 For tests on full data prior to release, [Nextflow Tower](https://tower.nf) launch feature can be employed.
 
 `awsfulltest.yml`: Triggers full sized tests run on AWS batch after releasing.
 
-* Must be only turned on for `release` and `workflow_dispatch`.
+* Must be turned on `workflow_dispatch`.
+* Must be turned on for `workflow_run` with `workflows: ["nf-core Docker push (release)"]` and `types: [completed]`
 * Should run the profile `test_full` that should be edited to provide the links to full-size datasets. If it runs the profile `test` a warning is given.
 
 ## Error #6 - Repository `README.md` tests ## {#6}

nf_core/__main__.py

@@ -34,7 +34,7 @@ def run_nf_core():
     rich.traceback.install(width=200, word_wrap=True)
 
     # Print nf-core header to STDERR
-    stderr = rich.console.Console(file=sys.stderr)
+    stderr = rich.console.Console(file=sys.stderr, force_terminal=nf_core.utils.rich_force_colors())
     stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False)
     stderr.print("[blue]          ___     __   __   __   ___     [green]/,-._.--~\\", highlight=False)
     stderr.print("[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
@@ -114,7 +114,7 @@ def nf_core_cli(verbose, log_file):
     log.addHandler(
         rich.logging.RichHandler(
             level=logging.DEBUG if verbose else logging.INFO,
-            console=rich.console.Console(file=sys.stderr),
+            console=rich.console.Console(file=sys.stderr, force_terminal=nf_core.utils.rich_force_colors()),
             show_time=False,
             markup=True,
         )

nf_core/launch.py

@@ -640,7 +640,7 @@ def validate_pattern(val):
     def print_param_header(self, param_id, param_obj):
         if "description" not in param_obj and "help_text" not in param_obj:
             return
-        console = Console()
+        console = Console(force_terminal=nf_core.utils.rich_force_colors())
         console.print("\n")
         console.print(param_obj.get("title", param_id), style="bold")
         if "description" in param_obj: