diff --git a/environment.yml b/environment.yml index bc6ee2cd..bd24fa3e 100644 --- a/environment.yml +++ b/environment.yml @@ -1,9 +1,9 @@ # to install this environment: -# micromamba create -f environment.yml +# micromamba create -f environment.yml -y name: open-gira channels: - - conda-forge - - bioconda + - conda-forge # majority of dependencies + - bioconda # snakemake - defaults dependencies: - python=3.10 @@ -12,6 +12,8 @@ dependencies: - nismod-snail==0.3.1 # vector-raster intersections - osmium==3.2.0 # OpenStreetMap protobuf handling - snkit==1.8.1 # spatial network cleaning + # required zenodo_get version not available via conda-forge + - zenodo_get>=1.5.1 # data download client, zenodo API broken w/ <1.5.1 - . # open_gira helper package - black # formatter - cython==0.29.28 # c--python interface @@ -19,7 +21,7 @@ dependencies: - datashader # plotting large datasets - flake8 # linter - gdal>=3.3 # command-line tools for spatial data - - geopandas>=0.11.0 # geospatial dataframes + - geopandas==0.14.1 # geospatial dataframes - geopy # geocoding client - ipykernel # notebook support - jupyter # notebook support @@ -32,7 +34,7 @@ dependencies: - openpyxl # Excel file format - osmium-tool==1.14.0 # openstreetmap extracts - pathos # multiprocessing - # test_network_components.py fails with 2.1.0, see commit msg + # test_network_components.py fails with pandas 2.1.0, see commit msg - pandas==2.0.3 # tabular data - pyarrow>=13.0.0 # parquet file format, Arrow data exchange - pyogrio # vectorised geospatial file i/o @@ -47,10 +49,9 @@ dependencies: - scipy # scientific computing library - spatialpandas # plotting large datasets - snakemake==7.18.2 # workflow management - - tabulate==0.8.10 # snakemake dependency with bug in 9.0.0, pin previous # https://github.com/snakemake/snakemake/issues/1891 + - tabulate==0.8.10 # snakemake dependency with bug in 9.0.0, pin previous - tqdm==4.62.3 # progress bars - wget # file downloader - # pin as 2023.11.0 will duplicate/nisname coords when concatenating + # pin xarray as suspect 2023.11.0 duplicates/nisnames coords when concatenating - xarray==2023.10.1 # named n-dimensional arrays - - zenodo_get # data download client