.

Author: lingfeiwang

.github/workflows/ci-conda.yml

@@ -28,10 +28,10 @@ jobs:
       version: ${{ steps.publish-pretest.outputs.version }}
       buildstr: ${{ steps.publish-pretest.outputs.buildstr }}
     steps:
-      - name: Set up Python 3.8
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.13
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
@@ -54,12 +54,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10"]
+        python-version: ["3.9","3.10","3.11"]
     steps:
-      - name: Set up Python 3.8
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.13
       - name: Add conda to system path
         shell: bash
         run: |
@@ -94,10 +94,10 @@ jobs:
     if: ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' )
     runs-on: ubuntu-latest
     steps:
-      - name: Set up Python 3.8
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.13
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0

.github/workflows/ci-inference.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10"]
+        python-version: ["3.9","3.10","3.11"]
         nth: ["2"]
     steps:
     - uses: actions/checkout@v4
@@ -53,7 +53,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10"]
+        python-version: ["3.9","3.10","3.11"]
         nth: ["1","2"]
     steps:
     - uses: actions/checkout@v4
@@ -84,7 +84,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10"]
+        python-version: ["3.9","3.10","3.11"]
         nth: ["2"]
     steps:
     - uses: actions/checkout@v4

.github/workflows/ci-install.yml

@@ -42,10 +42,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         ref: ${{ steps.version.outputs.version }}
-    - name: Set up Python 3.8
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.13
     - name: Obtain install script
       id: runscript
       run: |
@@ -83,10 +83,10 @@ jobs:
     runs-on: ubuntu-latest
     needs: install-script-bash
     steps:
-    - name: Set up Python 3.8
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
@@ -119,10 +119,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         ref: ${{ steps.version.outputs.version }}
-    - name: Set up Python 3.8
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.13
     - name: Obtain install script
       id: run0
       run: |
@@ -151,7 +151,7 @@ jobs:
         tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2
         s1="$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | grep '^[[:blank:]]' | sed 's/^[[:space:]]*//g')"
         #If failed here: update this line and the same line in /.github/actions/install-conda/action.yml to match the lines in /README.rst
-        cmp <(echo "$s1") <(echo "conda create -y -n dictys -c conda-forge python=3.9 mamba"; echo ". activate dictys"; echo "mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch dictys pytorch torchvision torchaudio cpuonly") || exit 1
+        cmp <(echo "$s1") <(echo "conda create -y -n dictys -c conda-forge python=3.10 mamba"; echo ". activate dictys"; echo "mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch dictys pytorch torchvision torchaudio cpuonly") || exit 1
         echo "run<<EOF" >> $GITHUB_ENV
         echo "$s1" >> $GITHUB_ENV
         echo "EOF" >> $GITHUB_ENV
@@ -165,10 +165,10 @@ jobs:
     runs-on: ubuntu-latest
     needs: install-script-conda
     steps:
-    - name: Set up Python 3.8
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
@@ -183,7 +183,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10",""]
+        python-version: ["3.9","3.10","3.11",""]
         cuda-version: ["11.7",""]
     steps:
     - name: Show version

README.rst

@@ -27,7 +27,7 @@ First install `Anaconda/Miniconda <https://docs.conda.io/en/latest/miniconda.htm
 
 .. code-block::
 
-	conda create -y -n dictys -c conda-forge python=3.9 mamba
+	conda create -y -n dictys -c conda-forge python=3.10 mamba
 	. activate dictys
 	mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch dictys pytorch torchvision torchaudio cpuonly
 
@@ -37,15 +37,15 @@ Alternatively, **with GPU computation** for PyTorch (here CUDA 11.7):
 
 .. code-block::
 
-	conda create -y -n dictys -c conda-forge python=3.9 mamba
+	conda create -y -n dictys -c conda-forge python=3.10 mamba
 	. activate dictys
 	mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch -c nvidia dictys pytorch torchvision torchaudio pytorch-cuda=11.7
 
 Or, with earlier versions (here CUDA 11.3, only supported in PyTorch 1):
 
 .. code-block::
 
-	conda create -y -n dictys -c conda-forge python=3.9 mamba
+	conda create -y -n dictys -c conda-forge python=3.10 mamba
 	. activate dictys
 	mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch -c nvidia dictys pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=11.3