From ac358fbeb94703b70353c5e01d7efcc34edcba54 Mon Sep 17 00:00:00 2001
From: floriscalkoen <floris_calkoen@hotmail.com>
Date: Wed, 9 Oct 2024 12:45:26 +0200
Subject: [PATCH] restore environment and readme from 80da1ae

---
 README.md       |  10 +--
 environment.yml | 228 ++++++++++++++++--------------------------------
 2 files changed, 75 insertions(+), 163 deletions(-)

diff --git a/README.md b/README.md
index ae92e62..93422f7 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,6 @@
 # coclico-workbench
 
-CoCliCo workbench prototype repository with tutorials & exploratory tools for Coastal
-Climate Core Services
-
-## Usage
-
-```bash
-mamba env create -f environment.yaml
-pip install -e /path/to/cloned/workbench/directory
-```
+CoCliCo workbench prototype repository with tutorials & exploratory tools for Coastal Climate Core Services
 
 ## Coding online in Google Colab
 
diff --git a/environment.yml b/environment.yml
index 5cd55da..4a5a48f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,178 +2,116 @@ name: coclico
 channels:
   - conda-forge
   - defaults
-
 dependencies:
-  # Basic tools
-  - python=3.12
+  - python=3.*
   - pip>=20
-  - setuptools
-  - conda-libmamba-solver
-  - ca-certificates
-  - certifi
-  - openssl
-  - boltons
-  - ciso8601
-  - cattrs
-
-# Development Tools
-  - bandit
-  - black
-  - click
-  - codespell
-  - flake8
-  - isort
-  - mypy
-  - nbsphinx
-  - poetry
-  - pre-commit
-  - pydantic
-  - pytest
-  - pytest-cov
-  - recommonmark
-  - ruff
-  - sphinx
-  - sphinx-autodoc-typehints
-  - sphinx-rtd-theme
-  - sphinx_rtd_theme
-  - python-dotenv
-
-  # Jupyter and extensions
-  - ipython
   - ipykernel
   - ipywidgets
-  - jupyter
-  - jupyterlab>=4
-  - jupyter-panel-proxy
-  - jupyter-resource-usage
-  - jupyterlab_code_formatter
-  - jupyterlab_execute_time
-  - jupyterlab_widgets
-  - jupyterlab-git
-  - jupyterlab-lsp
-  - jupyterlab-spellchecker
-  - nb_conda_kernels
-  - nbgitpuller
-  - nbstripout
-  - nodejs
-  - python-lsp-server
-  - voila
-  - jupyter-book
-  - nbformat
-  - dask-labextension
-  # - gh-scoped-creds # check if useful
-  # - lckr-jupyterlab-variableinspector  # doesn't work on my machine yet
-
-  # Interactive visualization libraries
-  - bokeh
-  - datashader
-  - firefox
-  - folium
-  - geckodriver
-  - geoviews
-  - holoviews
-  - hvplot
   - ipyleaflet
-  - ipympl
-  - jupyter_bokeh
-  - panel
-  - param
-  - selenium
-
-  # Standard sci-data analytics libs
-  - bottleneck
-  - cchardet
-  - numexpr
-  - fsspec
-  - intake
-  - jsonschema
-  - netcdf4
-  - numcodecs
-  - numpy
-  - opencv
-  - pandas
-  - pint
-  - polars
-  - pyarrow
-  - pyproj
-  - pyyaml
-  - scikit-image
-  - scikit-learn
-  - scipy
-  - toml
-  - xarray
-
-  # Cloud-related libraries
   - adlfs
+  - astropy
   - awscli
   - azure-data-tables
   - azure-identity
-  - boto3
-  - gcsfs
-  - google-cloud-storage
-  - s3fs
-
-  # Plotting libraries
-  - descartes
-  - matplotlib
-  - pillow
-  - seaborn
-
-  # Web-related libraries
+  - bandit
   - beautifulsoup4
-  - lxml
-  - requests
-
-  # Spatial libraries
-  - astropy
+  - black
+  - boltons
+  - boto3
   - cartopy
+  - cattrs
   - cfgrib
+  - cfchecker
+  - ciso8601
+  - click
+  - codespell
+  - colormaps
   - contextily
-  - dask[complete]
+  - dask
+  - dask-cloudprovider
+  - dask-gateway
   - dask-geopandas
   - dask-image
-  - dask-jobqueue
+  - dask-ml
   - datacube
+  - datashader
+  - defusedxml
+  - descartes
   - distributed
   - earthengine-api
   - eccodes>=2.24.2
-  - esda
+  - eodatasets3
   - fiona
+  - flake8
+  - folium
+  - fsspec
+  - gcsfs
   - geodatasets
   - geojson
   - geopandas>=0.11.0
-  - h3-py
-  - h3pandas
+  - geoviews-core
+  - google-cloud-storage
+  - h3
   - h5netcdf
   - h5py
-  - imbalanced-learn
+  - h5py
+  - holoviews
+  - hvplot
+  - intake
   - intake-esm
   - intake-geopandas
   - intake-stac
   - intake-xarray
-  - libpysal
+  - ipympl
+  - isort
+  - jsonschema
+  - jupyter-ui-poll
   - lmdb
+  - lxml
   - mapclassify
-  - mercantile
+  - matplotlib-base
+  - mypy
+  - nb_black
   - netcdf4
-  - odc-algo
+  - numcodecs
+  - numexpr
+  - numpy
   - odc-geo
   - odc-stac
-  - openpyxl
+  - opencv
+  - pandas
+  - panel
+  - param
   - pims
   - planetary-computer
   - pooch
+  - pre-commit
+  - pyam
   - pyarrow
-  - pyod
+  - pydantic
   - pyogrio
+  - pyrsistent
+  - pystac
+  - pytest
+  - pytest-cov
+  - python-dotenv
+  - python-graphviz
+  - python-rapidjson
+  - pyyaml
   - rasterio
-  - rio-cogeo
-  - rio-tiler
   - rioxarray
+  - s3fs
+  - scikit-image
+  - scikit-learn
+  - scipy
+  - seaborn
+  - slicerator
   - spatialpandas
+  - stac-geoparquet
   - stac-vrt
   - stackstac
   - stactools
+  - structlog
   - tabulate
   - tqdm
   - xarray
@@ -181,32 +119,14 @@ dependencies:
   - xvec
   - zarr
   - zstandard
-
-# other kind of libraries
-
-  - cfchecker
-  - colormaps
-  - defusedxml
-  - jupyter-ui-poll
-  - lmdb
-  - slicerator
-  - structlog
-  - python-rapidjson
-  - python-graphviz
-  - pyrsistent
-  - pyam
-  - eodatasets3
-
   - pip:
-      - antimeridian
-      - duckdb  # pypi has more recent releases
-      - movingpandas
-      - more-itertools
-      - networkx
-      - stac-geoparquet  # pypi has more recent releases
-      # - coclico  # probably better to install in dev mode (pip install -e .)
+      - stactools-geoparquet-items
+      - odc-ui
+      - odc-stac
+      - odc-stats
+      - odc-algo
+      - odc-io
+      - odc-cloud[ASYNC]
+      - mapbox # not sure if this is still being used
+      - mapboxcli # requires monkeypatch for Python 3.10
       - xstac
-    # Some useful odc libraries
-    # - dea-tools
-    # - odc-ui
-    # - odc-stats