Merge branch 'main' into main

.github/workflows/CI.yml

@@ -0,0 +1,101 @@
+name: Run Tests
+on:
+   pull_request:
+    branches:
+      - main
+   push:
+    branches:
+      - main
+    tags: '*'
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+       run:
+         shell: bash -el {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        python: [3.9]
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 🐍 ${{ matrix.python }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}  
+      - name: Create environment with micromamba 🐍🖤
+        uses: mamba-org/setup-micromamba@v1
+        with: 
+          micromamba-version: '1.3.1-0'
+          environment-file: ./environment.yml
+          environment-name: oggm_env                # it is recommendable to add both name and yml file. 
+          init-shell: bash
+          cache-environment: true
+#           condarc-file: ./condarc.yml                # If necessary, we can include .condarc to configure environment
+      - name: Test creation of environment with micromamba 🔧🐍🖤
+        run: | 
+            which python
+            conda env export
+        shell: bash -el {0}
+      - name: Update certifi
+        run: | 
+            pip install --upgrade certifi
+        shell: bash -el {0}
+#       - name: Test OGGM installation 🔧🌎 
+#         run: pytest.oggm
+#         shell: bash -el {0}
+      - name: Set ENV Variables for PyCall.jl 🐍 📞
+        run: export PYTHON=/home/runner/micromamba/envs/oggm_env/bin/python
+        shell: bash -el {0}
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+        with:
+          cache-registries: "true"
+          cache-compiled: "true"
+      - uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON : /home/runner/micromamba/envs/oggm_env/bin/python
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v3
+        with:
+          token: ${{secrets.CODECOV_TOKEN}}
+          files: lcov.info
+  # docs:
+  #   name: Documentation
+  #   runs-on: ubuntu-latest
+  #   permissions:
+  #     contents: write
+  #     statuses: write
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - uses: julia-actions/setup-julia@v1
+  #       with:
+  #         version: '1.9'
+  #     - uses: julia-actions/julia-buildpkg@v1
+  #       env:
+  #           PYTHON : /home/runner/micromamba/envs/oggm_env/bin/python
+  #     - uses: julia-actions/julia-docdeploy@v1
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #     - run: |
+  #         julia --project=docs -e '
+  #           using Documenter: DocMeta, doctest
+  #           using ODINN
+  #           DocMeta.setdocmeta!(ODINN, :DocTestSetup, :(using ODINN); recursive=true)
+  #           doctest(ODINN)'

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -17,11 +17,21 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Sleipnir = "f5e6c550-199f-11ee-3608-394420200519"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test"]
+
+[compat]
+OrdinaryDiffEq = "6"
+ProgressMeter = "1"
+PlotThemes = "3"
+Infiltrator = "1"
+Plots = "1"
+Tullio = "0.3"
+JLD2 = "0.4"
+Reexport = "1"
+PyCall = "1"

README.md

@@ -1,2 +1,3 @@
-# Huginn.jl
-Ice flow universal differential equations for ODINN.jl
+<img src="https://github.com/JordiBolibar/Huginn.jl/blob/main/data/Huginn_logo-20.png" width="250">
+
+Huginn.jl is a package containing all the glacier ice flow models and solvers for [ODINN.jl](https://github.com/ODINN-SciML/ODINN.jl). It also provides an accessible API to be easily used by other glacier models, such as the Open Global Glacier Model ([OGGM](https://github.com/OGGM/oggm)). This enables OGGM to access the high-performance glacier ice flow solvers in Julia in a seamless manner, via JuliaCall and PyCall.jl.  

environment.yml

@@ -0,0 +1,41 @@
+name: oggm_env
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - jupyter
+  - jupyterlab
+  - numpy
+  - scipy
+  - pandas
+  - shapely
+  - matplotlib
+  - Pillow
+  - netcdf4
+  - scikit-image
+  - scikit-learn
+  - configobj
+  - xarray
+  - pytest
+  - dask
+  - bottleneck
+  - gdal=3.3
+  - pyproj
+  - cartopy
+  - geopandas
+  - rasterio
+  - rioxarray
+  - pytables
+  - salem
+  - motionless
+  - ipython
+  - numpydoc
+  - seaborn
+  - pip
+  - pip:
+    - joblib
+    - progressbar2
+    - git+https://github.com/OGGM/pytest-mpl
+    - git+https://github.com/OGGM/massbalance-sandbox
+    - oggm==1.6.0
+    - certifi