From be157a8c7bc488d6dbeec471c61ef045b42efd77 Mon Sep 17 00:00:00 2001 From: isaacrobinson2000 Date: Thu, 4 Jan 2024 16:42:08 -0500 Subject: [PATCH] Seperate CPU-only mamba install config files. --- README.md | 8 +++- .../DIPLOMAT-DEEPLABCUT-CPU.yaml | 21 ++++++++ conda-environments/DIPLOMAT-SLEAP-CPU.yaml | 48 +++++++++++++++++++ docs/source/installation.rst | 11 ++++- 4 files changed, 85 insertions(+), 3 deletions(-) create mode 100644 conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml create mode 100644 conda-environments/DIPLOMAT-SLEAP-CPU.yaml diff --git a/README.md b/README.md index ca1910d..73d4900 100644 --- a/README.md +++ b/README.md @@ -39,12 +39,18 @@ pip install diplomat-track[dlc, gui] **NOTE:** DIPLOMAT also includes two environment configuration files for setting up DIPLOMAT with [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html), which can be installed on Windows, Linux, or MacOS using the [Miniforge](https://github.com/conda-forge/miniforge) installer. -To create an environment using mamba, run one of these two commands: +To create an environment using mamba, run one of these four commands: ```bash # Create the environment for using DIPLOMAT with DeepLabCut +# GPU: mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT.yaml +# CPU only: +mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml # OR Create an environment for using DIPLOMAT with SLEAP instead... +# GPU: mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP.yaml +# CPU only: +mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP-CPU.yaml ``` And then activate the environment with one of these two commands: ```bash diff --git a/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml b/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml new file mode 100644 index 0000000..93d44f3 --- /dev/null +++ b/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml @@ -0,0 +1,21 @@ +# Environment for using diplomat with DeepLabCut projects. +# Installs diplomat and DeepLabCut into the same environment. +name: DIPLOMAT-DEEPLABCUT +channels: + - conda-forge + - anaconda + - defaults +dependencies: + - python=3.9 + - pip + - ipython + - jupyter + - ffmpeg + - wxpython + - numpy<=1.20 + - numba + - tensorflow + - keras + - pip: + - deeplabcut + - diplomat-track diff --git a/conda-environments/DIPLOMAT-SLEAP-CPU.yaml b/conda-environments/DIPLOMAT-SLEAP-CPU.yaml new file mode 100644 index 0000000..48c4a25 --- /dev/null +++ b/conda-environments/DIPLOMAT-SLEAP-CPU.yaml @@ -0,0 +1,48 @@ +# Environment for using diplomat with SLEAP projects. +# Installs diplomat and SLEAP into the same environment. +name: DIPLOMAT-SLEAP + +channels: + - conda-forge + - nvidia + - anaconda + +dependencies: + - conda-forge::wxpython + - conda-forge::attrs >=21.2.0 #,<=21.4.0 + - conda-forge::cattrs ==1.1.1 + - conda-forge::imgaug ==0.4.0 + - conda-forge::jsmin + - conda-forge::jsonpickle ==1.2 + - conda-forge::networkx + - conda-forge::numpy >=1.19.5,<1.23.0 + - conda-forge::numba + - conda-forge::opencv + - conda-forge::pandas + - conda-forge::pip + - conda-forge::pillow #>=8.3.1,<=8.4.0 + - conda-forge::psutil + - conda-forge::pykalman + - conda-forge::pyside2 >=5.12 # To ensure application works correctly with QtPy. + - conda-forge::python >=3.8 # Run into _MAX_WINDOWS_WORKERS not found if == + - conda-forge::python-rapidjson + - conda-forge::pyyaml + - conda-forge::pyzmq + - conda-forge::qtpy >=2.0.1 + - conda-forge::rich + - conda-forge::scipy >=1.4.1,<=1.9.0 + - conda-forge::scikit-image + - conda-forge::scikit-learn ==1.0 + - conda-forge::scikit-video + - conda-forge::seaborn + - tensorflow >=2.6.0,<2.11 # No windows GPU support for >2.10 + - tensorflow-hub # Pinned in meta.yml, but no problems here... yet + + # Packages required by tensorflow to find/use GPUs + - conda-forge::cudatoolkit ==11.3.1 + # "==" results in package not found + - conda-forge::cudnn=8.2.1 + - nvidia::cuda-nvcc=11.3 + - pip: + - sleap + - diplomat-track \ No newline at end of file diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 6f9ec32..7b6c80d 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -28,11 +28,15 @@ With Support for DeepLabCut Projects Using Mamba or Conda ~~~~~~~~~~~~~~~~~~~~ -Once you have mamba or a mamba compatible CLI installed, you'll want to open a terminal and type: +Once you have mamba or a mamba compatible CLI installed, you'll want to open a terminal and type one of these +two commands: .. code-block:: sh + # Install diplomat with GPU support... mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT.yaml + # Install diplomat with CPU support only... + mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml .. hint:: @@ -73,11 +77,14 @@ With Support for SLEAP Projects Using Mamba or Conda ~~~~~~~~~~~~~~~~~~~~ -Once you have a mamba installed, you'll want to open a terminal and type: +Once you have a mamba installed, you'll want to open a terminal and type one of these two commands: .. code-block:: sh + # Install diplomat with GPU support... mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP.yaml + # Install diplomat with CPU support only... + mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP-CPU.yaml .. hint::