rationalize dependencies sources

Dockerfile

@@ -25,6 +25,7 @@ RUN curl -O https://confluence.ecmwf.int/download/attachments/45757960/eccodes-$
 
 RUN pip install --upgrade pip
 COPY requirements.txt /app/requirements.txt
+RUN pip config set global.find-links 'https://download.pytorch.org/whl/cu121 https://data.pyg.org/whl/torch-2.2.2+cu121.html'
 RUN set -eux && pip install --default-timeout=100 -r /app/requirements.txt
 COPY requirements_lint.txt /app/requirements_lint.txt
 RUN pip install --default-timeout=100 -r /app/requirements_lint.txt
@@ -45,9 +46,6 @@ RUN set -eux && groupadd --gid $USER_GUID $GROUPNAME \
     && echo "$USERNAME:$USERNAME" | chpasswd \
     && mkdir /run/sshd
 
-RUN set -eux && pip install pyg-lib==0.4.0 torch-scatter==2.1.2 torch-sparse==0.6.18 torch-cluster==1.6.2\
-    torch-geometric==2.3.1 -f https://data.pyg.org/whl/torch-2.1.2+cpu.html
-
 WORKDIR $HOME_DIR
 RUN curl -fsSL https://code-server.dev/install.sh | sh
 

README.md

@@ -104,7 +104,7 @@ For HPC, see the related doc (doc/installMF.md) to get the right installation se
 
 You can install a conda environment, including `py4cast` in editable mode, using
 ```sh
-conda env create --file env_conda.yaml
+conda env create --file env.yaml
 ```
 
 From an exixting conda environment, you can now install manually `py4cast` in development mode using

env.yaml

@@ -1,50 +1,11 @@
-name: nlam
+name: py4cast
 channels:
   - pytorch
-  - nvidia
-  - pyg
-  - conda-forge
-channel_priority: strict  
 dependencies:
   - python == 3.10.13
   - pytorch==2.2.2
-  - pyg==2.5.2  
-  - torchvision==0.17.2
-  - pytorch-cuda==12.1
-  - numpy>=1.24.2
-  - wandb>=0.13.10
-  - matplotlib>=3.7.0
-  - scipy>=1.10.0
-  - pytorch-lightning>=2.1.2
-  - lightning==2.2.4
-  - shapely>=2.0.1
-  - networkx>=3.0
-  - Cartopy>=0.22.0
-  - pyproj>=3.4.1
-  - plotly>=5.15.0
-  - tornado>=6.3.3
-  - cython>=3
-  - cfgrib==0.9.11.0
-  - dataclasses-json==0.6.4
-  - xarray==2024.5.0
-  - argparse-dataclass==2.0.0
-  - tensorboard==2.13.0
-  - typer==0.9.0
-  - netCDF4==1.6.5
-  - einops==0.7.0
-  - torchinfo==1.8.0
-  - tabulate==0.9.0
-  - pytest==8.1.1
-  - onnx==1.16.0
-  - onnxruntime==1.17.3
-  - monai==1.3.1
   - pip
   - pip:
-     - tensorboard-plugin-profile
-     - torch-tb-profiler==0.4.1
-     - tueplots>=0.0.8   
-     - onnxscript==0.1.0.dev20240421
-     - transformers==4.44.2
-     - gif==23.3.0
-     - scikit-image==0.24.0
-
+     - -r requirements.txt
+     - --find-links https://data.pyg.org/whl/torch-2.2.2.html
+     - --find-links https://download.pytorch.org/whl/cu121

requirements.txt

@@ -37,3 +37,8 @@ typer==0.9.0
 transformers==4.44.2
 tensorflow==2.13.1
 py-spy
+pyg-lib==0.4.0
+torch-scatter==2.1.2
+torch-sparse==0.6.18
+torch-cluster==1.6.2
+torch-geometric==2.3.1