v1.2.4 (#1030)

* fixed genomepy version

* fix chipseeker dependency warning

* update CHANGELOG

* fix docs

* update version

* replace missing assembly

* fix upsetplot warnings

* bump version

* typo

Author: siebrenf

.github/workflows/docs.yml

@@ -2,24 +2,27 @@ name: docs
 
 on:
   push:
+    branches: [ "master" , "develop" ]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
       - name: Install dependencies 🔨 & Build 🔧
         run: |
-          # setup mambaforge
-          wget -q -O Mambaforge.sh  "https://github.com/conda-forge/miniforge/releases/download/4.11.0-1/Mambaforge-$(uname)-$(uname -m).sh"
-          bash Mambaforge.sh -b -p "${HOME}/conda" > /dev/null
+          # setup miniforge
+          wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+          bash Miniforge3.sh -b -p "${HOME}/conda" > /dev/null
           source "${HOME}/conda/etc/profile.d/conda.sh"
           source "${HOME}/conda/etc/profile.d/mamba.sh"
           mamba activate
@@ -45,7 +48,7 @@ jobs:
           mamba env create --name seq2science --file doc_reqs.yaml
           rm doc_reqs.yaml
           mamba activate seq2science
-          pip3 install .
+          pip3 install . --no-deps --ignore-installed
 
           # make the docs
           python docs/scripts/schemas.py
@@ -55,7 +58,6 @@ jobs:
           sphinx-build docs/ build -W
           touch build/.nojekyll
 
-      # only deploy
       - name: Deploy 📬
         uses: JamesIves/github-pages-deploy-action@releases/v3
         if: github.ref == 'refs/heads/master'

CHANGELOG.md

@@ -9,7 +9,15 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate
 
 ## [Unreleased]
 
-## [1.2.3] - 2024-05-9
+## [1.2.4] - 2025-05-14
+
+### Fixed
+
+- updated genomepy version (works with all providers again)
+- fixed chipseeker warnings
+- fixed upsetplot warnings
+
+## [1.2.3] - 2025-05-9
 
 ### Fixed
 
@@ -849,7 +857,8 @@ Many minor bug- and quality of life fixes.
 
 First release of seq2science!
 
-[Unreleased]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.3...develop
+[Unreleased]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.4...develop
+[1.2.4]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.3...v1.2.4
 [1.2.3]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.2...v1.2.3
 [1.2.2]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.1...v1.2.2
 [1.2.1]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.0...v1.2.1

requirements.yaml

@@ -7,7 +7,7 @@ dependencies:
   - bioconda::snakemake-minimal=7.25.0
   - conda-forge::conda=24.1.2
   - conda-forge::mamba=1.5.9
-  - bioconda::genomepy=0.16.1
+  - bioconda::genomepy=0.16.2
   - conda-forge::biopython=1.81
   - conda-forge::filelock=3.10.7
   - conda-forge::pyyaml=6.0

seq2science/__init__.py

@@ -1,4 +1,4 @@
 from . import util
 
 __all__ = ["util"]
-__version__ = "1.2.2"
+__version__ = "1.2.4"

seq2science/envs/chipseeker.yaml

@@ -4,4 +4,5 @@ channels:
   - bioconda
 dependencies:
   - bioconda::bioconductor-chipseeker=1.42.0
+  - bioconda::bioconductor-txdbmaker=1.2.0
   - conda-forge::conda-ecosystem-user-package-isolation=1.0

seq2science/envs/upset.yaml

@@ -2,6 +2,7 @@ name: upset
 channels:
   - conda-forge
 dependencies:
-  - conda-forge::upsetplot=0.8.0
+  - conda-forge::upsetplot=0.9.0
+  - conda-forge::pandas=2.1.4
   - conda-forge::matplotlib-base=3.7.1
   - conda-forge::conda-ecosystem-user-package-isolation=1.0

seq2science/scripts/chipseeker.R

@@ -33,7 +33,7 @@ cat('\n')
 
 
 # load the gtf file and make it a txdb
-txdb_from_gtf <- makeTxDbFromGFF(gtf)
+txdb_from_gtf <- txdbmaker::makeTxDbFromGFF(gtf)
 
 peaks_list = list()
 for (i in seq_along(narrowpeaks)) {

seq2science/workflows/chip_seq/samples.tsv

@@ -3,7 +3,7 @@
 # https://vanheeringen-lab.github.io/seq2science/content/workflows/chip_seq.html#filling-out-the-samples-tsv
 # Make sure that you use tab as a delimiter
 sample	assembly	biological_replicates	descriptive_name	control
-GSM1689671	BDGP6.46	gd7ectoderm	gd7_ectodermal_rep1	GSM1689679
-GSM1689672	BDGP6.46	gd7ectoderm	gd7_ectodermal_rep2	GSM1689680
-GSM1689692	BDGP6.46	tl10bmesoderm	tl10b_mesodermal_rep1	GSM1689700
-GSM1689693	BDGP6.46	tl10bmesoderm	tl10b_mesodermal_rep2	GSM1689701
+GSM1689671	dm6	gd7ectoderm	gd7_ectodermal_rep1	GSM1689679
+GSM1689672	dm6	gd7ectoderm	gd7_ectodermal_rep2	GSM1689680
+GSM1689692	dm6	tl10bmesoderm	tl10b_mesodermal_rep1	GSM1689700
+GSM1689693	dm6	tl10bmesoderm	tl10b_mesodermal_rep2	GSM1689701