Merge pull request #741 from ScilifelabDataCentre/dev

New release: version 2.10.0

Author: i-oden

.github/pull_request_template.md

@@ -6,90 +6,92 @@
 4. When all boxes are checked, information is filled in, and the branch is updated: mark as Ready For Review and tag reviewers (top right)
 5. Once there is a submitted review, implement the suggestions (if reasonable, otherwise discuss) and request an new review.
 
-If there is a field which you are unsure about, enter the edit mode of this description or go to the [PR template](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/.github/pull_request_template.md); There are invisible comments providing descriptions which may be of help.
+If there is a field which you are unsure about, enter the edit mode of this description or go to the [PR template](../.github/pull_request_template.md); There are invisible comments providing descriptions which may be of help.
 
 ## 1. Description / Summary
 
-_Add a summary of the changes in this PR and the related issue._
+**Add a summary here**: What does this PR add/change and why?
 
 ## 2. Jira task / GitHub issue
 
-_Link to the github issue or add the Jira task ID here._
+**Is this a GitHub issue?** --> Add the link to the github issue
 
-## 3. Type of change
+**Is this from a Jira task?** --> If your branch does not contain info regarding the Jira task ID, put it here.
 
-What _type of change(s)_ does the PR contain?
+## 3. Type of change - Add label
 
-**Check the relevant boxes below. For an explanation of the different sections, enter edit mode of this PR description template.**
+**What _type of change(s)_ does the PR contain? For an explanation of the different options below, enter edit mode of this PR description template.**
 
-- [ ] New feature
-  - [ ] Breaking: _Why / How? Add info here._ <!-- Should be checked if the changes in this PR will cause existing functionality to not work as expected. E.g. with the master branch of the `dds_cli` -->
-  - [ ] Non-breaking <!-- Should be checked if the changes will not cause existing functionality to fail. "Non-breaking" is just an addition of a new feature. -->
-- [ ] Bug fix <!-- Should be checked when a bug is fixed in existing functionality. If the bug fix also is a breaking change (see above), add info about that beside this check box. -->
-- [ ] Security Alert fix <!-- Should be checked if the PR attempts to solve a security vulnerability, e.g. reported by the "Security" tab in the repo. -->
-  - [ ] Package update <!-- Should be checked if the Security alert fix consists of updating a package / dependency version -->
-    - [ ] Major version update <!-- Should be checked if the package / dependency version update is a major upgrade, e.g. 1.0.0 to 2.0.0 -->
-- [ ] Documentation <!-- Should be checked if the PR adds or updates the CLI documentation -- anything in docs/ directory. -->
-- [ ] Workflow <!-- Should be checked if the PR includes a change in e.g. the github actions files (dds_cli/.github/*) or another type of workflow change. Anything that alters our or the codes workflow. -->
-- [ ] Tests **only** <!-- Should only be checked if the PR only contains tests, none of the other types of changes listed above. -->
+_If you do not want this change to be included in release notes, add the label `skip-changelog`._
+
+- New feature
+  - Breaking --> label: `breaking` <!-- If the changes in this PR will cause existing functionality to not work as expected. E.g. with the master branch of the `dds_cli`. Add info here on how the change is breaking. -->
+  - Non-breaking --> label: `feature` <!-- If the changes will not cause existing functionality to fail. "Non-breaking" is just an addition of a new feature. -->
+- Database change --> label: `feature` or none at all.
+  _Remember the to include a new migration version, **or** explain here why it's not needed._ <!-- If you've changed something in `models.py`. For a guide on how to add the a new migration version, look at the "Database changes" section in the README.md. -->
+- Bug fix --> label: `bug` <!-- If a bug is fixed in existing functionality. If the bug fix also is a breaking change (see above), add info about that beside this check box. -->
+- Security Alert fix <!-- If the PR attempts to solve a security vulnerability, e.g. reported by the "Security" tab in the repo. -->
+  - Package update --> label: `dependency` <!-- If the Security alert fix consists of updating a package / dependency version -->
+    - Major version update <!-- If the package / dependency version update is a major upgrade, e.g. 1.0.0 to 2.0.0 -->
+- Documentation --> label can be skipped, will be included in "other changes" <!-- If the PR adds or updates the cli docs. -->
+- Workflow --> label: `skip-changelog` <!-- If the PR includes a change in e.g. the github actions files (dds_web/.github/*) or another type of workflow change. Anything that alters our or the codes workflow. -->
+- Tests **only** --> label: `skip-changelog` <!-- If the PR only contains tests, none of the other types of changes listed above. -->
 
 ## 4. Additional information
 
-- [ ] [Sprintlog](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/SPRINTLOG.md) <!-- Add a row at the bottom of the SPRINTLOG.md file (not needed if PR contains only tests). Follow the format of previous rows. If the PR is the first in a new sprint, add a new sprint header row (follow the format of previous sprints). -->
-- [ ] Blocking PRs <!-- Should be checked if there are blocking PRs or other tasks that need to be merged prior to this. Add link to PR or Jira card if this is the case. -->
-  - [ ] Merged <!-- Should be checked if the "Blocking PRs" box was checked AND all blocking PRs have been merged / fixed. -->
-- [ ] PR to `master` branch: _If checked, read [the release instructions](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/docs/procedures/new_release.md)_ <!-- Check this if the PR is made to the `master` branch. Only the `dev` branch should be doing this. -->
+- [ ] I have added an entry to the [Sprintlog](../SPRINTLOG.md) <!-- Add a row at the bottom of the SPRINTLOG.md file (not needed if PR contains only tests). Follow the format of previous rows. If the PR is the first in a new sprint, add a new sprint header row (follow the format of previous sprints). -->
+- [ ] This is a PR to the `master` branch: _If checked, read [the release instructions](../doc/procedures/new_release.md)_ <!-- Check this if the PR is made to the `master` branch. Only the `dev` branch should be doing this. -->
   - [ ] I have followed steps 1-8. <!-- Should be checked if the "PR to `master` branch" box is checked AND the specified steps in the release instructions have been followed. -->
 
 ## 5. Actions / Scans
 
-_Check the boxes when the specified checks have passed._
-
-**For information on what the different checks do and how to fix it if they're failing, enter edit mode of this description or go to the [PR template](https://github.com/ScilifelabDataCentre/dds_cli/blob/dev/.github/pull_request_template.md).**
+**Make sure that the following checks/actions have passed.**
 
-- [ ] **Black**
+- **Black**
 <!--
   What: Python code formatter.
   How to fix: Run `black .` locally to execute formatting.
 -->
-- [ ] **Pylint**
-<!--
-  What: Python code linter.
-  How to fix: Manually fix the code producing warnings. Code must get 10/10.
--->
-- [ ] **Prettier**
+- **Prettier**
 <!--
   What: General code formatter. Our use case: MD and yaml mainly.
   How to fix: Run npx prettier --write . locally to execute formatting.
 -->
-- [ ] **Yamllint**
+- **Pylint**
+<!--
+  What: Python code linter.
+  How to fix: Manually fix the code producing warnings. Code must get 10/10.
+-->
+- **Yamllint**
 <!--
   What: Linting of yaml files.
   How to fix: Manually fix any errors locally.
 -->
-- [ ] **Tests**
+- **Tests**
 <!--
   What: Pytest to verify that functionality works as expected.
   How to fix: Manually fix any errors locally. Follow the instructions in the "Run tests" section of the README.md to run the tests locally.
   Additional info: The PR should ALWAYS include new tests or fixed tests when there are code changes. When pytest action has finished, it will post a codecov report; Look at this report and verify the files you have changed are listed. "90% <100.00%> (+0.8%)" means "Tests cover 90% of the changed file, <100 % of this PR's code changes are tested>, and (the code changes and added tests increased the overall test coverage with 0.8%)
 -->
-- [ ] **TestPyPI**
-<!--
-  What: Builds the CLI and publishes to TestPyPI in order to verify before release.
-  How to fix: Check the action logs and fix potential issues manually.
--->
-- [ ] **CodeQL**
+- **CodeQL**
 <!--
   What: Scan for security vulnerabilities, bugs, errors.
   How to fix: Go through the alerts and either manually fix, dismiss or ignore. Add info on ignored or dismissed alerts.
 -->
-- [ ] **Trivy**
+- **Trivy**
 <!--
   What: Security scanner.
   How to fix: Go through the alerts and either manually fix, dismiss or ignore. Add info on ignored or dismissed alerts.
 -->
-- [ ] **Snyk**
+- **Snyk**
 <!--
   What: Security scanner.
   How to fix: Go through the alerts and either manually fix, dismiss or ignore. Add info on ignored or dismissed alerts.
 -->
+- **TestPyPI**
+<!--
+  What: Builds the CLI and publishes to TestPyPI in order to verify before release.
+  How to fix: Check the action logs and fix potential issues manually.
+-->
+
+If an action does not pass and you need help with how to solve it, enter edit mode of this PR template or go to the [PR template](../.github/pull_request_template.md).

.github/release.yml

@@ -0,0 +1,23 @@
+# file location/name: .github/release.yml
+changelog:
+  exclude:
+    labels: # A list of labels that exclude a pull request from appearing in release notes.
+      - skip-changelog
+    authors: # A list of user or bot login handles whose pull requests are to be excluded from release notes.
+      - dependabot[bot]
+  categories:
+    - title: 🚀 Features
+      labels:
+        - feature
+    - title: 🐛 Bug Fixes
+      labels:
+        - bug
+    - title: ⛓️‍💥 Breaking Changes
+      labels:
+        - breaking
+    - title: 🛡️ Dependencies
+      labels:
+        - dependency
+    - title: Other Changes
+      labels:
+        - "*" # Catch-all for pull requests that didn't match any of the previous categories

.github/workflows/docs-github-pages-cli.yml

@@ -13,7 +13,8 @@ jobs:
     name: Build the DDS CLI Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
       - name: Make dependencies available to Docker container
         run: |
           cat requirements.txt requirements-dev.txt > ./docs/requirements.txt

.github/workflows/pytest-cli.yml

@@ -12,10 +12,10 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v2
@@ -32,6 +32,7 @@ jobs:
           COVERAGE_FILE=./coverage/.coverage
           pytest --color=yes --cov=./dds_cli --cov-report=xml:coverage/report.xml
 
-      - uses: codecov/codecov-action@v2
+      - uses: codecov/codecov-action@v5
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage/report.xml

.github/workflows/release-cli.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
@@ -77,12 +77,12 @@ jobs:
               --exclude-module=tests --log-level INFO dds_cli/__init__.py
             OUT_FILE_NAME: dds_cli_win_x86_64.exe
             ASSET_MIME: application/vnd.microsoft.portable-executable
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             TARGET: Linux_x86_64
             CMD_BUILD: >
-              pyinstaller -F -c -n  dds_cli_ubuntu-20.04_x86_64 -i resources/scilifelab.icns
-              --exclude-module=tests  --target-arch x86_64 --log-level INFO dds_cli/__init__.py
-            OUT_FILE_NAME: dds_cli_ubuntu-20.04_x86_64
+              pyinstaller -F -c -n dds_cli_ubuntu-22.04_x86_64 -i resources/scilifelab.icns
+              --exclude-module=tests --target-arch x86_64 --log-level INFO dds_cli/__init__.py
+            OUT_FILE_NAME: dds_cli_ubuntu-22.04_x86_64
             ASSET_MIME: application/x-elf
           - os: ubuntu-latest # ubuntu-22.04 at the moment
             TARGET: Linux_x86_64
@@ -92,7 +92,7 @@ jobs:
             OUT_FILE_NAME: dds_cli_ubuntu-latest_x86_64
             ASSET_MIME: application/x-elf
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Python 3.9 setup
         uses: actions/setup-python@v4
         with:
@@ -124,7 +124,7 @@ jobs:
     needs: build-n-publish
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: Make dependencies available to Docker container
         run: |
           cat requirements.txt requirements-dev.txt > ./docs/requirements.txt

CHANGELOG.rst

@@ -1,6 +1,16 @@
 Changelog
 ==========
 
+.. _2.10.0:
+
+2.10.0 - 2025-04-08 
+~~~~~~~~~~~~~~~~~~~
+
+- 🚀 Features
+    - Inform users that data deletion with `dds data rm --rm-all` is queued; DDS handles deletion in background
+- Other Changes
+    - Fix CLI docs action
+
 .. _2.9.0:
 
 2.9.0 - 2024-12-18

README.md

@@ -23,12 +23,12 @@
 </a>
 <br />
 <a href="https://github.com/ScilifelabDataCentre/dds_cli/actions/workflows/lint-black-cli.yml">
-    <img alt="codecov" src="https://github.com/ScilifelabDataCentre/dds_cli/actions/workflows/lint-black-cli.yml/badge.svg?event=push">
+    <img alt="Formatter: black" src="https://github.com/ScilifelabDataCentre/dds_cli/actions/workflows/lint-black-cli.yml/badge.svg?event=push">
 </a>
 <img alt="CodeQL" src="https://github.com/ScilifelabDataCentre/dds_cli/actions/workflows/codeql-cli.yml/badge.svg">
-<a href="https://codecov.io/gh/ScilifelabDataCentre/dds_web">
-    <img alt="codecov" src="https://codecov.io/gh/ScilifelabDataCentre/dds_cli/branch/dev/graph/badge.svg?token=r5tM6o08Sd">
-</a>
+<a href="https://codecov.io/github/ScilifelabDataCentre/dds_cli" > 
+ <img src="https://codecov.io/github/ScilifelabDataCentre/dds_cli/graph/badge.svg?token=zsrDpNqs6v"/> 
+ </a>
 <img alt="Tests" src="https://github.com/ScilifelabDataCentre/dds_cli/actions/workflows/pytest-cli.yml/badge.svg">
 </p>
 

SPRINTLOG.md

@@ -397,3 +397,21 @@ _Empty sprint_
 # 2024-12-16 - 2024-12-20
 
 - New version: 2.9.0 ([#728](https://github.com/ScilifelabDataCentre/dds_cli/pull/728))
+- Include legacy packages (removed in Python 3.13) in development requirements to fix documentation on GitHub Pages ([#730](https://github.com/ScilifelabDataCentre/dds_cli/pull/730))
+
+# 2025-01-20 - 2025-01-31
+
+- Make release template ([#732](https://github.com/ScilifelabDataCentre/dds_cli/pull/732))
+- Fix codecov action ([#731](https://github.com/ScilifelabDataCentre/dds_cli/pull/731))
+
+# 2025-02-17 – 2025-02-28
+
+- Remove executable for Ubuntu 20.04 and add one for Ubuntu 22.04 ([#733](https://github.com/ScilifelabDataCentre/dds_cli/pull/733)).
+
+# 2025-03-17 – 2025-03-28
+
+- Inform users that data deletion has started when `dds data rm` is run ([#738](https://github.com/ScilifelabDataCentre/dds_cli/pull/738)).
+
+# 2025-03-31 - 2025-04-11
+
+- New version: 2.10.0 ([#742](https://github.com/ScilifelabDataCentre/dds_cli/pull/742))

dds_cli/data_remover.py

@@ -39,6 +39,7 @@ def __init__(
         self,
         project: str,
         method: str = "rm",
+        authenticate: bool = True,
         no_prompt: bool = False,
         token_path: str = None,
     ):
@@ -47,6 +48,7 @@ def __init__(
         super().__init__(
             project=project,
             method=method,
+            authenticate=authenticate,
             no_prompt=no_prompt,
             token_path=token_path,
         )
@@ -115,7 +117,6 @@ def delete_tempfile(file: pathlib.Path):
             LOG.warning("File deletion may have failed. Usage of space may increase.")
 
     # Public methods ###################### Public methods #
-    @removal_spinner
     def remove_all(self, *_, **__):
         """Remove all files in project."""
         # Perform request to API to perform deletion
@@ -128,12 +129,15 @@ def remove_all(self, *_, **__):
         )
 
         # Print out response - deleted or not?
-        if "removed" not in response_json:
+        queue_message: str = response_json.get("message")
+        if "removed" not in response_json or "message" not in response_json:
             raise dds_cli.exceptions.APIError(
                 "Malformatted response detected when attempting "
                 f"to remove all files from {self.project}."
             )
 
+        dds_cli.utils.console.print("\n" + queue_message)
+
     @removal_spinner
     def remove_file(self, files):
         """Remove specific files."""

dds_cli/version.py

@@ -2,4 +2,4 @@
 
 # Do not change bump the major version unless absolutely necessary - makes incompatible with API
 # If mid or minor version reaches 9, continue to 10, 11 etc.
-__version__ = "2.9.0"
+__version__ = "2.10.0"