Prepare for 3.2.0 release

mr-c commented 4 months ago

User description

Describe the change

Update version numbers for pending OpenMS 3.2.0 release

PR checklist

~~I have added description of the change I'm proposing in the OpenMS Documentation.~~
[x] I have read and followed OpenMS Documentation Contributing guidelines.
[ ] I have attached a screenshot of the relevant area after this change.
[x] CHANGELOG.md is updated.
[x] I have added my name in CONTRIBUTING.md.

PR Type

Documentation

Description

Updated version and release numbers in docs/conf.py for the upcoming 3.2.0 release.
Updated version number in CHANGELOG.md to reflect the new release.

Changes walkthrough 📝

Relevant files

Documentation

conf.py `Update version and release numbers in Sphinx configuration` docs/conf.py Updated `version` from '3.1.0' to '3.2.0'. Updated `release` from '3.1.0dev' to '3.2.0'.	+2/-2
CHANGELOG.md `Update version number in CHANGELOG` CHANGELOG.md - Changed version header from '3.1.0' to '3.2.0'.	+1/-1

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PR Reviewer Guide 🔍

⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Key issues to review

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PR Code Suggestions ✨

Category	Suggestion	Score
Enhancement	Enhance the detail in changelog entries for better clarity and information ___ Consider adding more detailed entries to the changelog to provide better insights into what has changed, improved, or been fixed in this version. [CHANGELOG.md [5]](https://github.com/OpenMS/OpenMS-docs/pull/234/files#diff-06572a96a58dc510037d5efa622f9bec8519bc1beab13c9f251e97e657a9d4edR5-R5) ```diff -- fix some TOPPAS inaccuracies +- Fixed inaccuracies in TOPPAS regarding XYZ feature, enhancing stability and performance. ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 9 Why: Providing more detailed changelog entries improves transparency and helps users understand the changes, improvements, and fixes in the new version.	9
Enhancement	Update the release status in the changelog to reflect the current stage more accurately ___ Update the release status in the changelog from 'under development' to a more specific status such as 'pending release' or 'released', depending on the actual status at the time of updating this file. [CHANGELOG.md [2]](https://github.com/OpenMS/OpenMS-docs/pull/234/files#diff-06572a96a58dc510037d5efa622f9bec8519bc1beab13c9f251e97e657a9d4edR2-R2) ```diff ----- OpenMS 3.2.0 (released: under development) ---- +---- OpenMS 3.2.0 (released: pending release) ---- ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 6 Why: Updating the release status to a more specific term like 'pending release' can provide better clarity, but it depends on the actual status at the time of the update.	6
Maintainability	Ensure consistency between version and release variables ___ Ensure that the version and release variables are updated together and match to avoid inconsistencies in documentation or build processes. [docs/conf.py [29-34]](https://github.com/OpenMS/OpenMS-docs/pull/234/files#diff-85933aa74a2d66c3e4dcdf7a9ad8397f5a7971080d34ef1108296a7c6b69e7e3R29-R34) ```diff +version = '3.2.0' +release = '3.2.0' - ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 8 Why: Ensuring that the version and release variables are updated together helps maintain consistency in documentation and build processes, which is crucial for maintainability.	8
Best practice	Add a development stage tag to the release version ___ Consider using a more descriptive tag for the release version to indicate the development stage or stability of the release (e.g., alpha, beta, rc). This can help in distinguishing between stable and development versions. [docs/conf.py [34]](https://github.com/OpenMS/OpenMS-docs/pull/234/files#diff-85933aa74a2d66c3e4dcdf7a9ad8397f5a7971080d34ef1108296a7c6b69e7e3R34-R34) ```diff -release = '3.2.0' +release = '3.2.0-beta' ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 7 Why: Adding a development stage tag can help distinguish between stable and development versions, which is a good practice. However, it may not be necessary if the release is already stable.	7

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CI Failure Feedback 🧐

**Action:** build-sphinx

**Failed stage:** [Run lychee](https://github.com/OpenMS/OpenMS-docs/actions/runs/9776308103/job/26988535799) [❌]

**Failure summary:** The action failed because there were network errors detected in the HTML files:
*
build/html/tutorials-and-quickstart-guides/openms-user-tutorial.html had a 403 Forbidden error for
the URL https://www.knime.org/downloads/overview.
*
build/html/getting-started/nextflow-get-started.html had a 404 Not Found error for the URL
https://nf-co.re/docs/usage/installation.
* build/html/tutorials/knime-user-tutorial.html had a 403
Forbidden error for the URL https://www.knime.org/downloads/overview.

Relevant error logs:

```yaml 1: ##[group]Operating System 2: Ubuntu ... 949: PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.11.9/x64/lib/pkgconfig 950: Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.9/x64 951: Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.9/x64 952: Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.9/x64 953: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.11.9/x64/lib 954: INPUT_GITHUB_TOKEN: 955: INPUT_ARGS: --cache --max-cache-age 1d './**/*.html' --timeout 40 956: INPUT_DEBUG: false 957: INPUT_FAIL: true ... 963: | Status | Count | 964: |---------------|-------| 965: | 🔍 Total | 8029 | 966: | ✅ Successful | 7732 | 967: | ⏳ Timeouts | 0 | 968: | 🔀 Redirected | 0 | 969: | 👻 Excluded | 294 | 970: | ❓ Unknown | 0 | 971: | 🚫 Errors | 3 | 972: ## Errors per input 973: ### Errors in build/html/tutorials-and-quickstart-guides/openms-user-tutorial.html 974: * [403] [https://www.knime.org/downloads/overview](https://www.knime.org/downloads/overview) | Failed: Network error: Forbidden 975: ### Errors in build/html/getting-started/nextflow-get-started.html 976: * [404] [https://nf-co.re/docs/usage/installation](https://nf-co.re/docs/usage/installation) | Failed: Network error: Not Found 977: ### Errors in build/html/tutorials/knime-user-tutorial.html 978: * [403] [https://www.knime.org/downloads/overview](https://www.knime.org/downloads/overview) | Failed: Network error: Forbidden 979: ##[error]Process completed with exit code 2. ```

✨ CI feedback usage guide:

The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).

timosachsenberg commented 4 months ago

can you give the lychee error messages a quick check if they are real? otherwise good to merge

codiumai-pr-agent-pro[bot] commented 4 months ago

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

**Action:** build-sphinx

**Failed stage:** [Run lychee](https://github.com/OpenMS/OpenMS-docs/actions/runs/9776308103/job/27202566677) [❌]

**Failure summary:** The action failed because there were 2 errors detected in the HTML files:
* The URL
https://www.knime.org/downloads/overview returned a 403 Forbidden error in the file
build/html/tutorials-and-quickstart-guides/openms-user-tutorial.html.
* The same URL
https://www.knime.org/downloads/overview also returned a 403 Forbidden error in the file
build/html/tutorials/knime-user-tutorial.html.

Relevant error logs:

```yaml 1: ##[group]Operating System 2: Ubuntu ... 947: PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.11.9/x64/lib/pkgconfig 948: Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.9/x64 949: Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.9/x64 950: Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.9/x64 951: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.11.9/x64/lib 952: INPUT_GITHUB_TOKEN: 953: INPUT_ARGS: --cache --max-cache-age 1d './**/*.html' --timeout 40 954: INPUT_DEBUG: false 955: INPUT_FAIL: true ... 961: | Status | Count | 962: |---------------|-------| 963: | 🔍 Total | 8029 | 964: | ✅ Successful | 7733 | 965: | ⏳ Timeouts | 0 | 966: | 🔀 Redirected | 0 | 967: | 👻 Excluded | 294 | 968: | ❓ Unknown | 0 | 969: | 🚫 Errors | 2 | 970: ## Errors per input 971: ### Errors in build/html/tutorials-and-quickstart-guides/openms-user-tutorial.html 972: * [403] [https://www.knime.org/downloads/overview](https://www.knime.org/downloads/overview) | Failed: Network error: Forbidden 973: ### Errors in build/html/tutorials/knime-user-tutorial.html 974: * [403] [https://www.knime.org/downloads/overview](https://www.knime.org/downloads/overview) | Failed: Network error: Forbidden 975: ##[error]Process completed with exit code 2. ```

✨ CI feedback usage guide:

The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).

mr-c commented 4 months ago

https://www.knime.com/downloads/overview is now a 403

Prior to this, and at least since October, 2017, it was a 301 redirect to https://www.knime.com/downloads/

https://web.archive.org/web/20171004005730/https://www.knime.com/downloads/overview

timosachsenberg commented 4 months ago

thanks for fixing the URL

OpenMS / OpenMS-docs