Merge branch 'main' into feature/cluster_execution

nismod · Nov 29, 2023 · b7a441c · b7a441c
2 parents c105026 + d97d2d6
commit b7a441c
Showing 1 changed file with 9 additions and 8 deletions.
diff --git 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
@@ -12,14 +12,16 @@ 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
   - contextily          # basemaps for plots
   - 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