From f390551ae4c9a445c9fde9219d0ee5984a8a22fb Mon Sep 17 00:00:00 2001 From: Zhang Yunjun Date: Fri, 9 Jul 2021 12:08:17 -0700 Subject: [PATCH] docs: standardize requirement files + rename the following files: - readthedocs.yml -> .readthedocs.yaml - docs/requirements.txt -> docs/requirements4rtd.txt - docs/conda.txt -> docs/requirements.txt - docs/conda_env.yml -> docs/environment.yml + update installation notes in mintpy installation page, circle CI and docker file. --- .circleci/config.yml | 2 +- readthedocs.yml => .readthedocs.yaml | 6 ++--- docker/Dockerfile | 2 +- docs/conda.txt | 26 ---------------------- docs/{conda_env.yml => environment.yml} | 6 ++--- docs/installation.md | 4 ++-- docs/requirements.txt | 29 +++++++++++++++++++------ docs/requirements4rtd.txt | 8 +++++++ 8 files changed, 40 insertions(+), 43 deletions(-) rename readthedocs.yml => .readthedocs.yaml (75%) delete mode 100644 docs/conda.txt rename docs/{conda_env.yml => environment.yml} (77%) create mode 100644 docs/requirements4rtd.txt diff --git a/.circleci/config.yml b/.circleci/config.yml index a2cf3ae94..d9dbc06b0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -39,7 +39,7 @@ jobs: git clone https://github.com/insarlab/PySolid.git ${HOME}/tools/PySolid # install dependencies source activate root - mamba install --verbose --yes --file ${MINTPY_HOME}/docs/conda.txt gdal>=3 fortran-compiler + mamba install --verbose --yes --file ${MINTPY_HOME}/docs/requirements.txt gdal>=3 fortran-compiler pip install git+https://github.com/tylere/pykml.git # compile pysolid Fortran code cd ${HOME}/tools/PySolid/pysolid diff --git a/readthedocs.yml b/.readthedocs.yaml similarity index 75% rename from readthedocs.yml rename to .readthedocs.yaml index 0326d725d..8c0cf1927 100644 --- a/readthedocs.yml +++ b/.readthedocs.yaml @@ -17,9 +17,9 @@ mkdocs: formats: all # Optionally set the version of Python and requirements required to build your docs +# conda method does not work because of the "command killed due to excessive memory consumption" error python: - version: 3.6 + version: 3.7 install: - - requirements: docs/requirements.txt + - requirements: docs/requirements4rtd.txt -formats: [] diff --git a/docker/Dockerfile b/docker/Dockerfile index 98d6318bf..9ec4aa567 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -55,7 +55,7 @@ RUN wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh && # Install dependencies RUN ${PYTHON3DIR}/bin/conda config --add channels conda-forge && \ - ${PYTHON3DIR}/bin/conda install --yes --file ${MINTPY_HOME}/docs/conda.txt + ${PYTHON3DIR}/bin/conda install --yes --file ${MINTPY_HOME}/docs/requirements.txt # Install pykml RUN ${PYTHON3DIR}/bin/pip install git+https://github.com/yunjunz/pykml.git diff --git a/docs/conda.txt b/docs/conda.txt deleted file mode 100644 index 90dc211a0..000000000 --- a/docs/conda.txt +++ /dev/null @@ -1,26 +0,0 @@ -python>=3.6,<3.9 -cartopy -cvxopt -dask>=1.0 -dask-jobqueue>=0.3 -defusedxml -h5py<3 -lxml -matplotlib -numpy -pip -pyproj -scikit-image -scipy -# pyaps dependencies -cdsapi -ecCodes -netcdf4 -pygrib -# pyhdf # required for MERRA, which is currently not supported in python3 version of pyaps -# pyresample dependencies -pyresample -openmp -pykdtree -xarray -zarr diff --git a/docs/conda_env.yml b/docs/environment.yml similarity index 77% rename from docs/conda_env.yml rename to docs/environment.yml index f99f86c57..a14f4d3d8 100644 --- a/docs/conda_env.yml +++ b/docs/environment.yml @@ -1,5 +1,5 @@ -# create environment : conda env create -f conda_env.yml -# update dependencies: conda env update -f conda_env.yml +# create environment : conda env create -f environment.yml +# update dependencies: conda env update -f environment.yml # remove environment : conda env remove -n mintpy # enter environment : conda activate mintpy # exit environment : conda deactivate @@ -32,7 +32,7 @@ dependencies: - ecCodes - netcdf4 - pygrib - - pyhdf + # - pyhdf # required by MERRA, which is currently not supported in pyaps3 # for pyresample - pyresample - openmp diff --git a/docs/installation.md b/docs/installation.md index 46a9c2a50..cc3f03a35 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -71,7 +71,7 @@ Run the following in your terminal to install the dependencies to your conda env # Add "gdal>=3" below to install extra dependencies if you use ARIA, FRInGE, HyP3 or GMTSAR # Add "isce2" below to install extra dependencies if you use ISCE-2 -conda install --yes -c conda-forge --file ~/tools/MintPy/docs/conda.txt +conda install --yes -c conda-forge --file ~/tools/MintPy/docs/requirements.txt $CONDA_PREFIX/bin/pip install git+https://github.com/insarlab/PySolid.git $CONDA_PREFIX/bin/pip install git+https://github.com/tylere/pykml.git @@ -80,7 +80,7 @@ $CONDA_PREFIX/bin/pip install git+https://github.com/tylere/pykml.git Or run the following in your terminal to install the dependencies to a new environment _**mintpy**_: ``` -conda env create -f $MINTPY_HOME/docs/conda_env.yml +conda env create -f $MINTPY_HOME/docs/environment.yml conda activate mintpy ``` diff --git a/docs/requirements.txt b/docs/requirements.txt index 75ddb079a..1bd338975 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,17 +1,32 @@ -# requirements.txt for readthedocs, which uses pip and could not handle python>=3.6 -# conda.txt for actual installation via conda -# conda_env.yml for actual installation via conda create environment -# ports.txt for actual installation via mac-ports -# setup.py for actual installation via pip [not finished yet] +# requirements4rtd.txt for readthedocs, which uses pip with limited memory usage +# requirements.txt for actual installation via conda +# environment.yml for actual installation via conda create environment +# ports.txt for actual installation via mac-ports +# setup.py for actual installation via pip [not finished yet] +python>=3.6,<3.9 +cartopy cvxopt dask>=1.0 dask-jobqueue>=0.3 defusedxml -h5py +h5py<3 lxml matplotlib numpy +pip pyproj -pyresample scikit-image scipy +# pyaps dependencies +cdsapi +ecCodes +netcdf4 +pygrib +# pyhdf # required by MERRA, which is currently not supported in pyaps3 +# pyresample dependencies +pyresample +openmp +pykdtree +xarray +zarr + diff --git a/docs/requirements4rtd.txt b/docs/requirements4rtd.txt new file mode 100644 index 000000000..cf41fbedd --- /dev/null +++ b/docs/requirements4rtd.txt @@ -0,0 +1,8 @@ +# requirements file to build Read the Docs ONLY +defusedxml +h5py +lxml +matplotlib +numpy +pyproj +scipy