[med-svn] [Git][med-team/metaphlan][upstream] 2 commits: New upstream version 4.0.4
harish chavre (@Harish1)
gitlab at salsa.debian.org
Thu May 22 07:11:39 BST 2025
harish chavre pushed to branch upstream at Debian Med / metaphlan
Commits:
264ade6e by Harish chavre at 2025-05-19T19:35:35+00:00
New upstream version 4.0.4
- - - - -
43294acf by Harish chavre at 2025-05-19T19:36:22+00:00
New upstream version 4.0.4
- - - - -
14 changed files:
- − .github/ISSUE_TEMPLATE/bug_report.md
- − .github/no-response.yml
- − .github/workflows/main.yml
- − .github/workflows/python-publish.yml
- − .github/workflows/pythonpackage.yml
- − .gitmodules
- + debian-tests-data/Test.fastq
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.1.bt2l
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.2.bt2l
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.3.bt2l
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.4.bt2l
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.pkl
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.rev.1.bt2l
- + debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.rev.2.bt2l
Changes:
=====================================
.github/ISSUE_TEMPLATE/bug_report.md deleted
=====================================
@@ -1,24 +0,0 @@
----
-name: Bug report
-about: Create a report to help us improve
-title: "[BUG]"
-labels: ''
-assignees: ''
-
----
-
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-**To Reproduce**
-Steps to reproduce the behavior:
-
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
-**Platform (please complete the following information):**
- - Version [e.g. 3.0]
- - Download source [e.g. pip]
-
-**Additional context**
-Add any other context about the problem here.
=====================================
.github/no-response.yml deleted
=====================================
@@ -1,9 +0,0 @@
-# Configuration for probot-no-response - https://github.com/probot/no-response
-
-# Number of days of inactivity before an Issue is closed for lack of response
-daysUntilClose: 14
-# Label requiring a response
-responseRequiredLabel: more-information-needed
-# Comment to post when closing an Issue for lack of response. Set to `false` to disable
-closeComment: >
- This issue has been automatically closed.
=====================================
.github/workflows/main.yml deleted
=====================================
@@ -1,16 +0,0 @@
-
-name: Close Issues
-on:
- issues:
- types: [opened]
-jobs:
- auto_close_all_issues:
- if: ${{ !github.event.issue.pull_request }}
- runs-on: ubuntu-latest
- steps:
- - uses: peter-evans/close-issue at v1
- with:
- comment: |
- Thank you for creating this issue.
- We currently field issues through our [bioBakery Discourse Support Forum](https://forum.biobakery.org/).
- If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.
=====================================
.github/workflows/python-publish.yml deleted
=====================================
@@ -1,31 +0,0 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: Upload Python Package
-
-on:
- release:
- types: [created]
-
-jobs:
- deploy:
-
- runs-on: ubuntu-latest
-
- steps:
- - uses: actions/checkout at v2
- - name: Set up Python
- uses: actions/setup-python at v2
- with:
- python-version: '3.7'
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- pip install setuptools wheel twine
- - name: Build and publish
- env:
- TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
- TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
- run: |
- python setup.py sdist bdist_wheel
- twine upload dist/*
=====================================
.github/workflows/pythonpackage.yml deleted
=====================================
@@ -1,40 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Build MetaPhlAn package
-
-on:
- push:
- branches: [ "master"]
- pull_request:
- branches: [ "master" ]
-
-jobs:
- build:
- runs-on: ubuntu-latest
- strategy:
- matrix:
- python-version: [ 3.7 ]
-
- steps:
- - uses: actions/checkout at v2
- - name: Set up Python 3.7
- uses: actions/setup-python at v1
- with:
- python-version: 3.7
- - name: Install dependencies
- run: |
- pip install numpy scipy cython
- sudo apt install bowtie2 muscle ncbi-blast+ raxml
- pip install .
- - name: Test
- run: |
- metaphlan -v
- strainphlan -h
- extract_markers.py -h
- merge_metaphlan_tables.py -h
- read_fastx.py -h
- add_metadata_tree.py -h
- plot_tree_graphlan.py -h
- sample2markers.py -h
- strain_transmission.py -h
=====================================
.gitmodules deleted
=====================================
@@ -1,10 +0,0 @@
-[submodule "metaphlan/utils/hclust2"]
-path = metaphlan/utils/hclust2
-url = https://github.com/SegataLab/hclust2
-
-[submodule "metaphlan/utils/cmseq"]
-path = metaphlan/utils/cmseq
-url = https://github.com/SegataLab/cmseq
-[submodule "phylophlan"]
-path = metaphlan/utils/phylophlan
-url = https://github.com/biobakery/phylophlan
=====================================
debian-tests-data/Test.fastq
=====================================
The diff for this file was not included because it is too large.
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.1.bt2l
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.1.bt2l differ
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.2.bt2l
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.2.bt2l differ
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.3.bt2l
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.3.bt2l differ
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.4.bt2l
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.4.bt2l differ
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.pkl
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.pkl differ
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.rev.1.bt2l
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.rev.1.bt2l differ
=====================================
debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.rev.2.bt2l
=====================================
Binary files /dev/null and b/debian-tests-data/mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910.rev.2.bt2l differ
View it on GitLab: https://salsa.debian.org/med-team/metaphlan/-/compare/dd4058b39b75ff7cfbc3bae92f08b49e38879901...43294acf80fdb8338c5274c157bf3e383e6ced23
--
View it on GitLab: https://salsa.debian.org/med-team/metaphlan/-/compare/dd4058b39b75ff7cfbc3bae92f08b49e38879901...43294acf80fdb8338c5274c157bf3e383e6ced23
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20250522/73d3e62e/attachment-0001.htm>
More information about the debian-med-commit
mailing list