TO REMOVE: test

Dockerfile

@@ -3,26 +3,32 @@ FROM mambaorg/micromamba:focal-cuda-11.3.1
 
 WORKDIR /app
 
-# use chown to prevent permission issues
-COPY --chown=$MAMBA_USER:$MAMBA_USER . .
-
 COPY environment.yml environment.yml
 
+USER root
+
 RUN micromamba env create -f /app/environment.yml
 
+USER $MAMBA_USER
+
 ENV PATH=$PATH:/opt/conda/envs/myria3d/bin/
 # Need to export this for torch_geometric to find where cuda is.
 # See https://github.com/pyg-team/pytorch_geometric/issues/2040#issuecomment-766610625
 ENV LD_LIBRARY_PATH="/opt/conda/envs/myria3d/lib/:$LD_LIBRARY_PATH"
 
-# Check success of environment creation.
-RUN python -c "import torch_geometric;"
+# # Check success of environment creation.
+# RUN python -c "import torch_geometric;"
+
+# use chown to prevent permission issues
+COPY --chown=$MAMBA_USER:$MAMBA_USER . .
 
 # locate proj
 ENV PROJ_LIB=/opt/conda/envs/myria3d/share/proj/
 
 # Check that myria3d can run
-RUN python run.py task.task_name=predict --help
+RUN python -c "print('bla')"
+
+# run.py task.task_name=predict --help
 
-# # Set the default command to bash for image inspection.
-# CMD ["bash"]
+# # # Set the default command to bash for image inspection.
+# # CMD ["bash"]

environment.yml

@@ -10,58 +10,58 @@ channels:
 dependencies:
   - python==3.9.*
   - pip
-  # --------- data formats --------- #
-  - numpy
-  - h5py
-  # --------- Deep Learning --------- #
-  # cudatoolkit to specify the cuda driver in the conda env
-  - conda-forge::cudatoolkit=11.3.1 # single equal sign there, not a typo
-  - pytorch::pytorch==1.11.0
-  - pytorch::torchvision==0.12.0
-  - conda-forge::pytorch-lightning==1.5.9
-  - conda-forge::torchmetrics==0.7.*
-  - comet_ml::comet_ml==3.31.*
-  - conda-forge::urllib3<2  # To solve for https://github.com/GeneralMills/pytrends/issues/591
-  - pyg::pytorch-cluster
-  - pyg::pytorch-scatter
-  - pyg::pytorch-sparse
-  - pyg::pyg==2.1.0
-    # Nota: if libcusparse.so.11. errors occur, run
-    # export LD_LIBRARY_PATH="/home/${USER}/miniconda/envs/lib:$LD_LIBRARY_PATH"
-    # ou
-    # export LD_LIBRARY_PATH="/home/${USER}/anaconda3/envs/lib:$LD_LIBRARY_PATH"
-    # see https://github.com/pyg-team/pytorch_geometric/issues/2040#issuecomment-766610625
-  # --------- geo --------- #
-  - pdal
-  - python-pdal
-  - pyproj
-    # --------- Visualization --------- #
-  - pandas
-  - matplotlib
-  # --------- loggers --------- #
-  # --------- linters --------- #
-  - pre-commit # hooks for applying linters on commit
-  - black # code formatting
-  - isort # import sorting
-  - flake8 # code analysis
-  # --------- tests --------- #
-  - pytest==7.1.*
-  - coverage==6.3.*
-  - pytest-cov==3.0.*
-  # --------- others --------- #
-  - python-dotenv # loading env variables from .env file
-  - rich # beautiful text formatting in terminal
-  - sh # for running bash commands in some tests
-  # - scikit-learn # used in some callbacks
-  - seaborn # used in some callbacks
-  # - jupyterlab # better jupyter notebooks
-  - pudb # debugger
-    # # --------- Documentation --------- #
-  - sphinx==4.5.*
-  - recommonmark==0.7.*
-  - sphinx_rtd_theme==1.0.*
-  - docutils==0.17
-  - rstcheck==3.3.*  # RST Linter
+  # # --------- data formats --------- #
+  # - numpy
+  # - h5py
+  # # --------- Deep Learning --------- #
+  # # cudatoolkit to specify the cuda driver in the conda env
+  # - conda-forge::cudatoolkit=11.3.1 # single equal sign there, not a typo
+  # - pytorch::pytorch==1.11.0
+  # - pytorch::torchvision==0.12.0
+  # - conda-forge::pytorch-lightning==1.5.9
+  # - conda-forge::torchmetrics==0.7.*
+  # - comet_ml::comet_ml==3.31.*
+  # - conda-forge::urllib3<2  # To solve for https://github.com/GeneralMills/pytrends/issues/591
+  # - pyg::pytorch-cluster
+  # - pyg::pytorch-scatter
+  # - pyg::pytorch-sparse
+  # - pyg::pyg==2.1.0
+  #   # Nota: if libcusparse.so.11. errors occur, run
+  #   # export LD_LIBRARY_PATH="/home/${USER}/miniconda/envs/lib:$LD_LIBRARY_PATH"
+  #   # ou
+  #   # export LD_LIBRARY_PATH="/home/${USER}/anaconda3/envs/lib:$LD_LIBRARY_PATH"
+  #   # see https://github.com/pyg-team/pytorch_geometric/issues/2040#issuecomment-766610625
+  # # --------- geo --------- #
+  # - pdal
+  # - python-pdal
+  # - pyproj
+  #   # --------- Visualization --------- #
+  # - pandas
+  # - matplotlib
+  # # --------- loggers --------- #
+  # # --------- linters --------- #
+  # - pre-commit # hooks for applying linters on commit
+  # - black # code formatting
+  # - isort # import sorting
+  # - flake8 # code analysis
+  # # --------- tests --------- #
+  # - pytest==7.1.*
+  # - coverage==6.3.*
+  # - pytest-cov==3.0.*
+  # # --------- others --------- #
+  # - python-dotenv # loading env variables from .env file
+  # - rich # beautiful text formatting in terminal
+  # - sh # for running bash commands in some tests
+  # # - scikit-learn # used in some callbacks
+  # - seaborn # used in some callbacks
+  # # - jupyterlab # better jupyter notebooks
+  # - pudb # debugger
+  #   # # --------- Documentation --------- #
+  # - sphinx==4.5.*
+  # - recommonmark==0.7.*
+  # - sphinx_rtd_theme==1.0.*
+  # - docutils==0.17
+  # - rstcheck==3.3.*  # RST Linter
   - pip:
       # --------- hydra configs --------- #
     - hydra-core==1.1.*