ci(linting): add remaining linting and formatting checks

.editorconfig

@@ -0,0 +1,17 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace=true
+
+[*.{css,html,js,json,scss,yaml,yml}]
+indent_size = 2
+
+[*.{py,sh}]
+indent_size = 4
+
+[*.go]
+indent_style = tab

.github/workflows/ci.yml

@@ -114,6 +114,77 @@ jobs:
           pip install check-manifest
           ./run-tests.sh --check-manifest
 
+  lint-jsonlint:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+
+      - name: Lint JSON files
+        run: |
+          npm install jsonlint --global
+          ./run-tests.sh --check-jsonlint
+
+  lint-markdownlint:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+
+      - name: Lint Markdown files
+        run: |
+          npm install markdownlint-cli2 --global
+          ./run-tests.sh --check-markdownlint
+
+  format-shfmt:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Check shell script code formatting
+        run: |
+          sudo apt-get install shfmt
+          ./run-tests.sh --check-shfmt
+
+  format-prettier:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+
+      - name: Check Prettier code fomatting
+        run: |
+          npm install prettier --global
+          ./run-tests.sh --check-prettier
+
+  lint-yamllint:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Lint YAML files
+        run: |
+          pip install yamllint
+          ./run-tests.sh --check-yamllint
+
   docs-sphinx:
     runs-on: ubuntu-24.04
     steps:
@@ -186,8 +257,7 @@ jobs:
   release-docker:
     runs-on: ubuntu-24.04
     if: >
-      vars.RELEASE_DOCKER == 'true' &&
-      github.event_name == 'push' &&
+      vars.RELEASE_DOCKER == 'true' && github.event_name == 'push' &&
       startsWith(github.ref, 'refs/tags/')
     needs:
       - docs-sphinx

.markdownlint.yaml

@@ -0,0 +1,5 @@
+# Allow prompt dollar sign in console examples without showing output
+MD014: false
+
+# Allow multiple headings with same content (for different releases)
+MD024: false

.prettierignore

@@ -0,0 +1,3 @@
+.pytest_cache
+CHANGELOG.md
+docs/openapi.json

.prettierrc.yaml

@@ -0,0 +1,2 @@
+printWidth: 80
+proseWrap: always

.release-please-config.json

@@ -5,9 +5,13 @@
     ".": {
       "changelog-sections": [
         { "type": "build", "section": "Build", "hidden": false },
-        { "type": "feat", "section": "Features", "hidden": false  },
+        { "type": "feat", "section": "Features", "hidden": false },
         { "type": "fix", "section": "Bug fixes", "hidden": false },
-        { "type": "perf", "section": "Performance improvements", "hidden": false },
+        {
+          "type": "perf",
+          "section": "Performance improvements",
+          "hidden": false
+        },
         { "type": "refactor", "section": "Code refactoring", "hidden": false },
         { "type": "style", "section": "Code style", "hidden": false },
         { "type": "test", "section": "Test suite", "hidden": false },

.yamllint.yaml

@@ -0,0 +1,8 @@
+extends: default
+
+rules:
+  comments:
+    min-spaces-from-content: 1
+  document-start: disable
+  line-length: disable
+  truthy: disable

AUTHORS.md

@@ -6,6 +6,7 @@ The list of contributors in alphabetical order:
 - [Agisilaos Kounelis](https://orcid.org/0000-0001-9312-3189)
 - [Anton Khodak](https://orcid.org/0000-0003-3263-4553)
 - [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663)
+- [Cameron McClymont](https://orcid.org/0009-0002-0176-5251)
 - [Camila Diaz](https://orcid.org/0000-0001-5543-797X)
 - [Dan Leehr](https://orcid.org/0000-0003-3221-9579)
 - [Daniel Prelipcean](https://orcid.org/0000-0002-4855-194X)

CHANGELOG.md

@@ -1,39 +1,35 @@
+<!-- markdownlint-disable MD013 -->
+
 # Changelog
 
 ## [0.9.4](https://github.com/reanahub/reana-workflow-engine-cwl/compare/0.9.3...0.9.4) (2024-11-29)
 
-
 ### Build
 
 * **docker:** pin setuptools 70 ([#287](https://github.com/reanahub/reana-workflow-engine-cwl/issues/287)) ([3c2cd8a](https://github.com/reanahub/reana-workflow-engine-cwl/commit/3c2cd8a474d167574bf8746b6430f4ae13a83e61))
 * **python:** bump shared REANA packages as of 2024-11-28 ([#289](https://github.com/reanahub/reana-workflow-engine-cwl/issues/289)) ([f9d3688](https://github.com/reanahub/reana-workflow-engine-cwl/commit/f9d3688858e6f1ff52fa58fecd9ce233dd97b0e1))
 
-
 ### Features
 
 * **task:** allow Compute4PUNCH backend options ([#277](https://github.com/reanahub/reana-workflow-engine-cwl/issues/277)) ([9b2a3d0](https://github.com/reanahub/reana-workflow-engine-cwl/commit/9b2a3d0872329e79d0b2d9a0972b0c09f08ff694))
 
 ## [0.9.3](https://github.com/reanahub/reana-workflow-engine-cwl/compare/0.9.2...0.9.3) (2024-03-04)
 
-
 ### Build
 
 * **docker:** install correct extras of reana-commons submodule ([#261](https://github.com/reanahub/reana-workflow-engine-cwl/issues/261)) ([21957fe](https://github.com/reanahub/reana-workflow-engine-cwl/commit/21957fe41921d9c557067b2773205af6385f755b))
 * **docker:** non-editable submodules in "latest" mode ([#255](https://github.com/reanahub/reana-workflow-engine-cwl/issues/255)) ([a6acc88](https://github.com/reanahub/reana-workflow-engine-cwl/commit/a6acc888a36694e3306993cfc3108752b60bd1f3))
 * **python:** bump all required packages as of 2024-03-04 ([#267](https://github.com/reanahub/reana-workflow-engine-cwl/issues/267)) ([ed6a846](https://github.com/reanahub/reana-workflow-engine-cwl/commit/ed6a846eb1d8a0bf92f77906749b5853e5794114))
 * **python:** bump shared REANA packages as of 2024-03-04 ([#267](https://github.com/reanahub/reana-workflow-engine-cwl/issues/267)) ([47155ef](https://github.com/reanahub/reana-workflow-engine-cwl/commit/47155ef95c4eb19642dd54a732402b2551973658))
 
-
 ### Bug fixes
 
 * **progress:** handle stopped jobs ([#260](https://github.com/reanahub/reana-workflow-engine-cwl/issues/260)) ([bc36cb7](https://github.com/reanahub/reana-workflow-engine-cwl/commit/bc36cb7813a20fde685a40694af0732ded483d3a))
 
-
 ### Code refactoring
 
 * **docs:** move from reST to Markdown ([#263](https://github.com/reanahub/reana-workflow-engine-cwl/issues/263)) ([3cf272f](https://github.com/reanahub/reana-workflow-engine-cwl/commit/3cf272f657cc3e0b329c6d159f5e476f06000f93))
 
-
 ### Continuous integration
 
 * **commitlint:** addition of commit message linter ([#256](https://github.com/reanahub/reana-workflow-engine-cwl/issues/256)) ([021854e](https://github.com/reanahub/reana-workflow-engine-cwl/commit/021854e309999938cf01c31bda5ab095679e03b0))
@@ -43,119 +39,118 @@
 * **release-please:** update version in Dockerfile ([#259](https://github.com/reanahub/reana-workflow-engine-cwl/issues/259)) ([0961257](https://github.com/reanahub/reana-workflow-engine-cwl/commit/096125709172e6bea1510a9fd2fdcb90299fac8b))
 * **shellcheck:** fix exit code propagation ([#262](https://github.com/reanahub/reana-workflow-engine-cwl/issues/262)) ([6568b9b](https://github.com/reanahub/reana-workflow-engine-cwl/commit/6568b9b229141dd8dd2a261a833057358143590f))
 
-
 ### Documentation
 
 * **authors:** complete list of contributors ([#266](https://github.com/reanahub/reana-workflow-engine-cwl/issues/266)) ([2960cd9](https://github.com/reanahub/reana-workflow-engine-cwl/commit/2960cd9c06a8e12283822ec9fbf87aba7b9b9fb5))
 * **conformance-tests:** update CWL conformance test badges ([#264](https://github.com/reanahub/reana-workflow-engine-cwl/issues/264)) ([45afa2e](https://github.com/reanahub/reana-workflow-engine-cwl/commit/45afa2efd984fd84bbae48fde6ca663f70dd86dc))
 
 ## 0.9.2 (2023-12-12)
 
-- Adds automated multi-platform container image building for amd64 and arm64 architectures.
-- Adds metadata labels to Dockerfile.
-- Fixes container image building on the arm64 architecture.
+* Adds automated multi-platform container image building for amd64 and arm64 architectures.
+* Adds metadata labels to Dockerfile.
+* Fixes container image building on the arm64 architecture.
 
 ## 0.9.1 (2023-09-27)
 
-- Fixes container image names to be Podman-compatible.
+* Fixes container image names to be Podman-compatible.
 
 ## 0.9.0 (2023-01-19)
 
-- Adds support for specifying `slurm_partition` and `slurm_time` for Slurm compute backend jobs.
-- Adds support for Kerberos authentication for workflow orchestration.
-- Adds support for Rucio authentication for workflow jobs.
-- Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.
-- Fixes status reporting for failed jobs that were incorrectly considered successful.
+* Adds support for specifying `slurm_partition` and `slurm_time` for Slurm compute backend jobs.
+* Adds support for Kerberos authentication for workflow orchestration.
+* Adds support for Rucio authentication for workflow jobs.
+* Changes the base image of the component to Ubuntu 20.04 LTS and reduces final Docker image size by removing build-time dependencies.
+* Fixes status reporting for failed jobs that were incorrectly considered successful.
 
 ## 0.8.1 (2022-02-07)
 
-- Adds support for specifying `kubernetes_job_timeout` for Kubernetes compute backend jobs.
+* Adds support for specifying `kubernetes_job_timeout` for Kubernetes compute backend jobs.
 
 ## 0.8.0 (2021-11-22)
 
-- Adds support for custom workspace paths.
-- Adds supoort for `cwltool` version `3.1.20210628163208`
+* Adds support for custom workspace paths.
+* Adds supoort for `cwltool` version `3.1.20210628163208`
 
 ## 0.7.6 (2021-07-05)
 
-- Changes internal dependencies to remove click.
+* Changes internal dependencies to remove click.
 
 ## 0.7.5 (2021-04-28)
 
-- Adds support for specifying `kubernetes_memory_limit` for Kubernetes compute backend jobs.
+* Adds support for specifying `kubernetes_memory_limit` for Kubernetes compute backend jobs.
 
 ## 0.7.4 (2021-03-23)
 
-- Changes job command serialisation using central REANA-Commons job command serialiser.
+* Changes job command serialisation using central REANA-Commons job command serialiser.
 
 ## 0.7.3 (2021-03-17)
 
-- Changes workflow engine instantiation to use central REANA-Commons factory.
-- Changes status `succeeded` to `finished` to use central REANA nomenclature.
+* Changes workflow engine instantiation to use central REANA-Commons factory.
+* Changes status `succeeded` to `finished` to use central REANA nomenclature.
 
 ## 0.7.2 (2021-02-03)
 
-- Fixes minor code warnings.
-- Changes CI system to include Python flake8 and Dockerfile hadolint checkers.
+* Fixes minor code warnings.
+* Changes CI system to include Python flake8 and Dockerfile hadolint checkers.
 
 ## 0.7.1 (2020-11-10)
 
-- Adds support for specifying `htcondor_max_runtime` and `htcondor_accounting_group` for HTCondor compute backend jobs.
-- Fixes restarting of CWL workflows.
+* Adds support for specifying `htcondor_max_runtime` and `htcondor_accounting_group` for HTCondor compute backend jobs.
+* Fixes restarting of CWL workflows.
 
 ## 0.7.0 (2020-10-20)
 
-- Adds pinning of all Python dependencies allowing to easily rebuild component images at later times.
-- Adds option to specify unpacked Docker images as workflow step requirement.
-- Adds support for handling new workflow operational options.
-- Adds support for VOMS proxy as a new authentication method.
-- Changes base image to use Python 3.8.
-- Changes code formatting to respect `black` coding style.
-- Changes documentation to single-page layout.
+* Adds pinning of all Python dependencies allowing to easily rebuild component images at later times.
+* Adds option to specify unpacked Docker images as workflow step requirement.
+* Adds support for handling new workflow operational options.
+* Adds support for VOMS proxy as a new authentication method.
+* Changes base image to use Python 3.8.
+* Changes code formatting to respect `black` coding style.
+* Changes documentation to single-page layout.
 
 ## 0.6.1 (2020-05-25)
 
-- Upgrades REANA-Commons package using latest Kubernetes Python client version.
+* Upgrades REANA-Commons package using latest Kubernetes Python client version.
 
 ## 0.6.0 (2019-12-20)
 
-- Allows to specify compute backend (HTCondor, Kubernetes or Slurm) and
+* Allows to specify compute backend (HTCondor, Kubernetes or Slurm) and
   Kerberos authentication requirement for CWL workflow jobs.
-- Upgrades cwltool to 1.0.20191022103248.
-- Moves workflow engine to the same Kubernetes pod with the REANA-Job-Controller
+* Upgrades cwltool to 1.0.20191022103248.
+* Moves workflow engine to the same Kubernetes pod with the REANA-Job-Controller
   (sidecar pattern).
 
 ## 0.5.0 (2019-04-23)
 
-- Makes workflow engine independent of Celery so that independent workflow
+* Makes workflow engine independent of Celery so that independent workflow
   instances are created on demand for each user.
-- Replaces `api_client` module with centralised one from REANA-Commons.
-- Introduces CVMFS mounts in job specifications.
-- Sets default file mode creation mask to 002 so that workflows are able to
+* Replaces `api_client` module with centralised one from REANA-Commons.
+* Introduces CVMFS mounts in job specifications.
+* Sets default file mode creation mask to 002 so that workflows are able to
   write to shared directories for any user identity under which the workflow
   processes may be running.
-- Makes docker image slimmer by using `python:2.7-slim`.
-- Centralises log level and log format configuration.
-- Upgrades cwltool to 1.0.20181118133959.
+* Makes docker image slimmer by using `python:2.7-slim`.
+* Centralises log level and log format configuration.
+* Upgrades cwltool to 1.0.20181118133959.
 
 ## 0.4.0 (2018-11-06)
 
-- Improves AMQP re-connection handling. Switches from `pika` to `kombu`.
-- Utilises common openapi client for communication with REANA-Job-Controller.
-- Changes license to MIT.
+* Improves AMQP re-connection handling. Switches from `pika` to `kombu`.
+* Utilises common openapi client for communication with REANA-Job-Controller.
+* Changes license to MIT.
 
 ## 0.3.2 (2018-09-25)
 
-- Upgrades to latest `cwltool` (`1.0.20180912090223`).
+* Upgrades to latest `cwltool` (`1.0.20180912090223`).
 
 ## 0.3.1 (2018-09-07)
 
-- Pins REANA-Commons dependency.
+* Pins REANA-Commons dependency.
 
 ## 0.3.0 (2018-08-10)
 
-- Tracks progress of workflow runs.
+* Tracks progress of workflow runs.
 
 ## 0.2.0 (2018-04-19)
 
-- Initial public release.
+* Initial public release.

CONTRIBUTING.md

@@ -1,11 +1,12 @@
 # Contributing
 
-Bug reports, issues, feature requests, and other contributions are welcome. If you find
-a demonstrable problem that is caused by the REANA code, please:
+Bug reports, issues, feature requests, and other contributions are welcome. If
+you find a demonstrable problem that is caused by the REANA code, please:
 
-1. Search for [already reported problems](https://github.com/reanahub/reana-workflow-engine-cwl/issues).
-2. Check if the issue has been fixed or is still reproducible on the
-   latest `master` branch.
+1. Search for
+   [already reported problems](https://github.com/reanahub/reana-workflow-engine-cwl/issues).
+2. Check if the issue has been fixed or is still reproducible on the latest
+   `master` branch.
 3. Create an issue, ideally with **a test case**.
 
 If you create a pull request fixing a bug or implementing a feature, you can run

MANIFEST.in

@@ -18,6 +18,9 @@ include docs/requirements.txt
 include pytest.ini
 include scripts/*.py
 exclude .readthedocs.yaml
+exclude .editorconfig
+exclude .prettierrc.yaml
+exclude .prettierignore
 prune docs/_build
 recursive-include badges *.json
 recursive-include docs *.py