Updated to match new zenodo URLs.

Recovered matplotlib version.

.github/actions/zenodo-url-translate/action.yml

@@ -1,4 +1,4 @@
-# Lingfei Wang, 2022. All rights reserved.
+# Lingfei Wang, 2022, 2023. All rights reserved.
 name: Translate Zenodo URL to follow the latest DOI version 
 
 inputs:
@@ -20,8 +20,10 @@ runs:
       run: |
         set -eo pipefail
         s0='${{ inputs.url }}'
-        s1="$(curl -Ls -o /dev/null -w %{url_effective} "$s0")"
-        s2="$s1/${s0#http[s]*://zenodo.org/record/[^/]*/}"
+        s2="${s0#http[s]*://zenodo.org/records/[^/]*/}"
+        s1="${s0%/$s2}"
+        s1="$(curl -Ls -o /dev/null -w %{url_effective} "$s1")"
+        s2="$s1/$s2"
         echo "Old URL: $s0"
         echo "New URL: $s2"
         echo "url=$s2" >> $GITHUB_OUTPUT

.github/workflows/ci-conda.yml

@@ -74,7 +74,7 @@ jobs:
         id: zenodo-url-translate
         uses: ./.github/actions/zenodo-url-translate
         with:
-          url: https://zenodo.org/record/6858494/files/inference-blood1.tar.xz?download=1
+          url: https://zenodo.org/records/6858494/files/inference-blood1.tar.xz?download=1
       - name: Test dataset
         uses: ./.github/actions/inference-test-dataset
         with:

.github/workflows/ci-container.yml

@@ -48,7 +48,7 @@ jobs:
         id: zenodo-url-translate
         uses: ./.github/actions/zenodo-url-translate
         with:
-          url: https://zenodo.org/record/6858494/files/inference-blood1.tar.xz?download=1
+          url: https://zenodo.org/records/6858494/files/inference-blood1.tar.xz?download=1
       - name: Test dataset
         uses: ./.github/actions/inference-test-dataset
         with:

.github/workflows/ci-inference.yml

@@ -33,7 +33,7 @@ jobs:
       id: zenodo-url-translate
       uses: ./.github/actions/zenodo-url-translate
       with:
-        url: https://zenodo.org/record/6858494/files/inference-skin1.tar.xz?download=1
+        url: https://zenodo.org/records/6858494/files/inference-skin1.tar.xz?download=1
     - name: Test dataset
       uses: ./.github/actions/inference-test-dataset
       with:
@@ -63,7 +63,7 @@ jobs:
       id: zenodo-url-translate
       uses: ./.github/actions/zenodo-url-translate
       with:
-        url: https://zenodo.org/record/6858494/files/inference-blood1.tar.xz?download=1
+        url: https://zenodo.org/records/6858494/files/inference-blood1.tar.xz?download=1
     - name: Test dataset
       uses: ./.github/actions/inference-test-dataset
       with:
@@ -93,7 +93,7 @@ jobs:
       id: zenodo-url-translate
       uses: ./.github/actions/zenodo-url-translate
       with:
-        url: https://zenodo.org/record/6858494/files/inference-blood2.tar.xz?download=1
+        url: https://zenodo.org/records/6858494/files/inference-blood2.tar.xz?download=1
     - name: Test dataset
       uses: ./.github/actions/inference-test-dataset
       with:

doc/scripts/install.sh

@@ -78,7 +78,6 @@ if [ "a$STEPS" == "a" ] || [ "a$(( STEPS & 2 ))" != "a0" ]; then
 		pip install $PIP_OPTIONS --no-deps pyDNase "$LOCAL_VERSION"
 	fi
 	pip install $PIP_OPTIONS $(pip check | grep ', which is not installed[.]$' | awk -F ',' '{print $(NF-1)}' | awk '{print $NF}' | grep -vi '^pyDNase$')
-	pip install $PIP_OPTIONS matplotlib==3.7.1
 fi
 if [ "a$STEPS" == "a" ] || [ "a$(( STEPS & 4 ))" != "a0" ]; then
 	#Update homer

setup.py

@@ -23,7 +23,7 @@ def pkg_setup():
 		long_description_content_type='text/x-rst',
 		url=url,
 		scripts=['bin/dictys','bin/dictys_helper'],
-		install_requires=['numpy','pandas','docutils','h5py','pyro-ppl','scipy','networkx','pybedtools','pyDNase','threadpoolctl','joblib','torch','matplotlib==3.7.1','adjustText','jupyter'],
+		install_requires=['numpy','pandas','docutils','h5py','pyro-ppl','scipy','networkx','pybedtools','pyDNase','threadpoolctl','joblib','torch','matplotlib','adjustText','jupyter'],
 		classifiers=[
 			'Development Status :: 5 - Production/Stable',
 			'Environment :: Console',

src/dictys/chromatin.py

@@ -187,7 +187,7 @@ def _motif_postproc(dret,fi_exp:str,fo_bed:str,fo_wellington:str,fo_homer:str)->
 	#Remove motifs having no TF in current dataset
 	t1=[not x.startswith('_') for x in namem]
 	dw,dh=[x[:,t1] for x in [dw,dh]]
-	namem,=namem[t1]
+	namem=namem[t1]
 	if len(namem)!=len(set(namem)):
 		from collections import Counter
 		t1=[x[0] for x in Counter(namem).items() if x[1]>1][:3]

utils/conda/meta.yaml

@@ -50,7 +50,7 @@ requirements:
     - pyDNase
     - threadpoolctl
     - joblib
-    - matplotlib ==3.7.1
+    - matplotlib
     - jupyter
     - adjustText