ci(markdownlint): add Markdown linting checks (#254)

Author: tiborsimko

.github/workflows/ci.yml

@@ -119,6 +119,20 @@ jobs:
           pip install flake8
           ./run-tests.sh --lint-flake8
 
+  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 --lint-markdownlint
+
   lint-manifest:
     runs-on: ubuntu-24.04
     steps:

.markdownlint.yaml

@@ -0,0 +1,2 @@
+# Allow prompt dollar sign in console examples without showing output
+MD014: false

CHANGELOG.md

@@ -1,31 +1,29 @@
+<!-- markdownlint-disable MD013 -->
+<!-- markdownlint-disable MD024 -->
+
 # Changelog
 
 ## [0.9.5](https://github.com/reanahub/reana-db/compare/0.9.4...0.9.5) (2024-11-26)
 
-
 ### Features
 
 * **cli:** add new `migrate-secret-key` command ([#240](https://github.com/reanahub/reana-db/issues/240)) ([efcbe72](https://github.com/reanahub/reana-db/commit/efcbe724a2797edf94a531a2fd49ae0dc25d29f7))
 
-
 ### Continuous integration
 
 * **actions:** pin setuptools 70 ([#239](https://github.com/reanahub/reana-db/issues/239)) ([3202759](https://github.com/reanahub/reana-db/commit/320275969c64513f695ce59a145088f6222aa594))
 * **python:** test more Python versions ([#239](https://github.com/reanahub/reana-db/issues/239)) ([e0cba7f](https://github.com/reanahub/reana-db/commit/e0cba7faa97cbf2919c4008ec884ea46ec817cd5))
 
 ## [0.9.4](https://github.com/reanahub/reana-db/compare/0.9.3...0.9.4) (2024-03-01)
 
-
 ### Code refactoring
 
 * **docs:** move from reST to Markdown ([#225](https://github.com/reanahub/reana-db/issues/225)) ([b48eb55](https://github.com/reanahub/reana-db/commit/b48eb55f7a1b1bbdde0e0a458852349a439a511e))
 
-
 ### Code style
 
 * **black:** format with black v24 ([#224](https://github.com/reanahub/reana-db/issues/224)) ([cc60522](https://github.com/reanahub/reana-db/commit/cc6052242fd14cf3413b793d0aa32a24871fe1b1))
 
-
 ### Continuous integration
 
 * **commitlint:** addition of commit message linter ([#218](https://github.com/reanahub/reana-db/issues/218)) ([ee0f7e5](https://github.com/reanahub/reana-db/commit/ee0f7e5e106e0be619779bfa2133415feecc323b))
@@ -35,133 +33,132 @@
 * **release-please:** initial configuration ([#218](https://github.com/reanahub/reana-db/issues/218)) ([7c616d6](https://github.com/reanahub/reana-db/commit/7c616d67fac642656f56d37422ba69c4a8d4fa20))
 * **shellcheck:** fix exit code propagation ([#223](https://github.com/reanahub/reana-db/issues/223)) ([b62ee1e](https://github.com/reanahub/reana-db/commit/b62ee1e3be44628265bf5ada7e0b7eb88e283c00))
 
-
 ### Documentation
 
 * **authors:** complete list of contributors ([#227](https://github.com/reanahub/reana-db/issues/227)) ([3fbcf65](https://github.com/reanahub/reana-db/commit/3fbcf65db735146d54078cae4c5b9c8968ead055))
 
 ## 0.9.3 (2023-12-01)
 
-- Changes the `Workflow` table to replace the `run_number` column with two new columns `run_number_major` and `run_number_minor` in order to allow for more than nine restarts of user workflows.
-- Changes the names of database table, column, index and key constraints in order to follow the SQLAlchemy upstream naming conventions everywhere.
-- Changes several database index definitions in order to improve performance of most common database queries.
+* Changes the `Workflow` table to replace the `run_number` column with two new columns `run_number_major` and `run_number_minor` in order to allow for more than nine restarts of user workflows.
+* Changes the names of database table, column, index and key constraints in order to follow the SQLAlchemy upstream naming conventions everywhere.
+* Changes several database index definitions in order to improve performance of most common database queries.
 
 ## 0.9.2 (2023-09-26)
 
-- Adds progress meter to the logs of the periodic quota updater.
-- Changes CPU and disk quota calculations to improve the performance of periodic quota updater.
-- Fixes the workflow priority calculation to avoid workflows stuck in the `queued` status when the number of allowed concurrent workflow is set to zero.
+* Adds progress meter to the logs of the periodic quota updater.
+* Changes CPU and disk quota calculations to improve the performance of periodic quota updater.
+* Fixes the workflow priority calculation to avoid workflows stuck in the `queued` status when the number of allowed concurrent workflow is set to zero.
 
 ## 0.9.1 (2023-01-18)
 
-- Changes to PostgreSQL 12.13.
-- Fixes conversion of possibly-negative resource usage values to human-readable formats.
-- Fixes disk quota updater to prevent setting negative disk quota usage values.
-- Fixes quota updater to reduce memory usage.
+* Changes to PostgreSQL 12.13.
+* Fixes conversion of possibly-negative resource usage values to human-readable formats.
+* Fixes disk quota updater to prevent setting negative disk quota usage values.
+* Fixes quota updater to reduce memory usage.
 
 ## 0.9.0 (2022-12-13)
 
-- Adds new `launcher_url` column to the `Workflow` table to store the remote origin of workflows submitted via the Launch-on-REANA functionality.
-- Adds the possibility to force resource quota updates irrespective of globally-configured quota update policy.
-- Adds new `WorkspaceRetentionRule` table to store workspace file retention rules.
-- Adds new `WorkspaceRetentionAuditLog` table to store the audit log of workspace file retention rule updates.
-- Changes percentage ranges used to calculate the health status of user resource quota usage.
-- Changes to PostgreSQL 12.10.
-- Fixes wrong numbering of restarted workflows by limiting the number of times a workflow can be restarted to nine.
-- Fixes `Workflow.get_workspace_disk_usage` to always calculate disk usage rather than relying on the quota usage values from the database, since these may not be up-to-date depending on the global quota update policy.
-- Fixes helper function that retrieves workflows by UUID to also additionally check that the provided user is the owner of the workflow.
+* Adds new `launcher_url` column to the `Workflow` table to store the remote origin of workflows submitted via the Launch-on-REANA functionality.
+* Adds the possibility to force resource quota updates irrespective of globally-configured quota update policy.
+* Adds new `WorkspaceRetentionRule` table to store workspace file retention rules.
+* Adds new `WorkspaceRetentionAuditLog` table to store the audit log of workspace file retention rule updates.
+* Changes percentage ranges used to calculate the health status of user resource quota usage.
+* Changes to PostgreSQL 12.10.
+* Fixes wrong numbering of restarted workflows by limiting the number of times a workflow can be restarted to nine.
+* Fixes `Workflow.get_workspace_disk_usage` to always calculate disk usage rather than relying on the quota usage values from the database, since these may not be up-to-date depending on the global quota update policy.
+* Fixes helper function that retrieves workflows by UUID to also additionally check that the provided user is the owner of the workflow.
 
 ## 0.8.2 (2022-02-23)
 
-- Adds transition for workflow from queued to failed status.
+* Adds transition for workflow from queued to failed status.
 
 ## 0.8.1 (2022-02-01)
 
-- Adds an option to periodically calculate CPU quota usage.
-- Changes CLI quota command from `disk-usage-update` to `resource-usage-update` since it can also perform CPU quota calculation.
-- Fixes quota update functions to handle exceptional situation as continuable errors.
-- Removes extra `QuotaResourceType` enum in favor of `ResourceType.name`.
+* Adds an option to periodically calculate CPU quota usage.
+* Changes CLI quota command from `disk-usage-update` to `resource-usage-update` since it can also perform CPU quota calculation.
+* Fixes quota update functions to handle exceptional situation as continuable errors.
+* Removes extra `QuotaResourceType` enum in favor of `ResourceType.name`.
 
 ## 0.8.0 (2021-11-22)
 
-- Adds new disk usage retrieval methods using canonical (bytes) and human-readable (KiB) units. (`User`, `Workflow`)
-- Adds Quota models which calculates CPU and disk usage.
-- Adds `InteractiveSession` model.
-- Adds new properties `started_at` and `finished_at` to the `Job` model, updated on status change.
-- Adds `get_priority` workflow method, that combines both complexity and concurrency, to pass to the scheduler.
-- Adds a possibility to configure database connection pool parameters via environment variables.
-- Adds new `pending` state to `RunStatus` table.
-- Adds workflow complexity property in `Workflow` table.
-- Adds environment variable to configure which quotas to update.
-- Changes `WorkflowStatus` table to `RunStatus`.
-- Changes disk quota calculation functions to allow passing raw bytes to increase the used quota.
-- Changes to PostgreSQL 12.8.
-- Removes support for Python 2.
+* Adds new disk usage retrieval methods using canonical (bytes) and human-readable (KiB) units. (`User`, `Workflow`)
+* Adds Quota models which calculates CPU and disk usage.
+* Adds `InteractiveSession` model.
+* Adds new properties `started_at` and `finished_at` to the `Job` model, updated on status change.
+* Adds `get_priority` workflow method, that combines both complexity and concurrency, to pass to the scheduler.
+* Adds a possibility to configure database connection pool parameters via environment variables.
+* Adds new `pending` state to `RunStatus` table.
+* Adds workflow complexity property in `Workflow` table.
+* Adds environment variable to configure which quotas to update.
+* Changes `WorkflowStatus` table to `RunStatus`.
+* Changes disk quota calculation functions to allow passing raw bytes to increase the used quota.
+* Changes to PostgreSQL 12.8.
+* Removes support for Python 2.
 
 ## 0.7.3 (2021-03-17)
 
-- Fixes REANA installation by pinning SQLAlchemy version less than 1.4.0 due to <https://github.com/kvesteri/sqlalchemy-utils/issues/505>.
+* Fixes REANA installation by pinning SQLAlchemy version less than 1.4.0 due to <https://github.com/kvesteri/sqlalchemy-utils/issues/505>.
 
 ## 0.7.2 (2021-02-22)
 
-- Adds utility to status enums to decide whether to clean workflows and jobs depending on their status.
+* Adds utility to status enums to decide whether to clean workflows and jobs depending on their status.
 
 ## 0.7.1 (2021-02-02)
 
-- Adds support for Python 3.9.
-- Fixes minor code warnings.
-- Changes CI system to include Python flake8 checker.
+* Adds support for Python 3.9.
+* Fixes minor code warnings.
+* Changes CI system to include Python flake8 checker.
 
 ## 0.7.0 (2020-10-20)
 
-- Adds initial central workflow status transition logic handler.
-- Adds new audit table and logic to register actions. (`AuditLog`, `AuditLogAction`)
-- Adds fixtures for better testing of database models.
-- Changes user token storage to move tokens from `User` table to `UserToken` table and to encrypt them.
-- Changes `Workflow` table to add a new `workspace_path` column.
-- Changes default database service to use centrally configured one from REANA-Commons. (`REANA_INFRASTRUCTURE_COMPONENTS_HOSTNAMES`)
-- Changes code formatting to respect `black` coding style.
-- Changes documentation to single-page layout.
+* Adds initial central workflow status transition logic handler.
+* Adds new audit table and logic to register actions. (`AuditLog`, `AuditLogAction`)
+* Adds fixtures for better testing of database models.
+* Changes user token storage to move tokens from `User` table to `UserToken` table and to encrypt them.
+* Changes `Workflow` table to add a new `workspace_path` column.
+* Changes default database service to use centrally configured one from REANA-Commons. (`REANA_INFRASTRUCTURE_COMPONENTS_HOSTNAMES`)
+* Changes code formatting to respect `black` coding style.
+* Changes documentation to single-page layout.
 
 ## 0.6.0 (2019-12-19)
 
-- Adds new method which returns full workflow name.
-- Adds more granular DB configuration.
-- Adds Git repository information to the workflow model.
+* Adds new method which returns full workflow name.
+* Adds more granular DB configuration.
+* Adds Git repository information to the workflow model.
   (`Workflow.git_repo`, `Workflow.git_provider`)
-- Adds user name information to the user model.
+* Adds user name information to the user model.
   (`User.full_name`, `User.username`)
-- Removes restart count information from the job model.
+* Removes restart count information from the job model.
   (`Job.restart_count`, `Job.max_restart_count`)
-- Adds support for Python 3.8.
+* Adds support for Python 3.8.
 
 ## 0.5.0 (2019-04-16)
 
-- Introduces new workflow statuses: `deleted`, `stopped`, `queued`.
-- Adds new field to store workflow stopping time. (`Workflow.run_stopped_at`)
-- Moves workflow input parameters to its own column to separate them from
+* Introduces new workflow statuses: `deleted`, `stopped`, `queued`.
+* Adds new field to store workflow stopping time. (`Workflow.run_stopped_at`)
+* Moves workflow input parameters to its own column to separate them from
   operational options. Adapts getters accordingly.
   (`Workflow.input_parameters`)
-- Adds new method to retrieve the workflow owner's token.
+* Adds new method to retrieve the workflow owner's token.
   (`Workflow.get_owner_access_token`)
-- Introduces new utility function to retrieve workflows by `uuid` or name.
+* Introduces new utility function to retrieve workflows by `uuid` or name.
   (`_get_workflow_with_uuid_or_name`)
-- Introduces new fields for interactive sessions: `interactive_session`,
+* Introduces new fields for interactive sessions: `interactive_session`,
   `interactive_session_name` and `interactive_session_type`. Note that with
   current design only one interactive session per workflow is supported.
-- Adds a new enumeration for possible job statuses. (`JobStatus`)
-- Adds new field to identify jobs in the underlying compute backend.
+* Adds a new enumeration for possible job statuses. (`JobStatus`)
+* Adds new field to identify jobs in the underlying compute backend.
   (`Job.backend_job_id`)
 
 ## 0.4.0 (2018-11-06)
 
-- Stores `reana.yaml` in database models.
-- Adds Workflow specification and parameter getters.
-- Adds support for Python 3.7.
-- Changes license to MIT.
+* Stores `reana.yaml` in database models.
+* Adds Workflow specification and parameter getters.
+* Adds support for Python 3.7.
+* Changes license to MIT.
 
 ## 0.3.0 (2018-08-10)
 
-- This package is a result of refactoring [reana-commons](https://reana-commons.readthedocs.io/).
-- Provides common REANA models.
-- Provides database connection logic.
+* This package is a result of refactoring [reana-commons](https://reana-commons.readthedocs.io/).
+* Provides common REANA models.
+* Provides database connection logic.

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # 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-db/issues).
 2. Check if the issue has been fixed or is still reproducible on the

docs/index.md

@@ -1,6 +1,10 @@
+<!-- markdownlint-disable MD041 -->
+<!-- markdownlint-disable MD033 -->
+
 % The title is set to `REANA-DB docs` instead of `REANA-DB` as this is a
 % workaround to avoid having multiple HTML objects with the same id/anchor,
 % as the tile clashes with the CLI API documentation generated by sphinx_click
+
 # REANA-DB docs
 
 ```{include} ../README.md

run-tests.sh

@@ -109,6 +109,10 @@ lint_manifest() {
     check-manifest
 }
 
+lint_markdownlint() {
+    markdownlint-cli2 "**/*.md"
+}
+
 lint_pydocstyle() {
     pydocstyle reana_db
 }
@@ -137,6 +141,7 @@ all() {
     lint_flake8
     lint_jsonlint
     lint_manifest
+    lint_markdownlint
     lint_pydocstyle
     lint_shellcheck
     lint_yamllint
@@ -155,6 +160,7 @@ help() {
     echo "  --lint-flake8        Check linting of Python code"
     echo "  --lint-jsonlint      Check linting of JSON files"
     echo "  --lint-manifest      Check linting of Python manifest"
+    echo "  --lint-markdownlint  Check linting of Markdown files"
     echo "  --lint-pydocstyle    Check linting of Python docstrings"
     echo "  --lint-shellcheck    Check linting of shell scripts"
     echo "  --lint-yamllint      Check linting of YAML files"
@@ -177,6 +183,7 @@ case $arg in
 --lint-flake8) lint_flake8 ;;
 --lint-jsonlint) lint_jsonlint ;;
 --lint-manifest) lint_manifest ;;
+--lint-markdownlint) lint_markdownlint ;;
 --lint-pydocstyle) lint_pydocstyle ;;
 --lint-shellcheck) lint_shellcheck ;;
 --lint-yamllint) lint_yamllint ;;