Adding Sphinx documentation (#2)

* Updating github actions to use single build script

* Adding basic sphinx docs

* Changing fabm-ersem to pyfabm-ersem

* Adding famb0d-gotm-ersem build

* Seperating README into sphinx docs

* Adding pyfabm tutorial script

* Restructure tutorial page

* Updating install scripts into seperate folders

* Running pyfabm-tut on github actions

* Initial restructure of sphinx docs

* Adding basic api

* Updating api generator

* Updating pyfabm tutorial

* Updating api

* Renaming api to module index

* Updating structure

* Updating history.rst and adding description from webpage pdf

* Updating gotm tutorial

* Updating ERSEM model pages

* Updating tutorials

* Adding gotm tutorial to actions

* Adding netcdf install to gotm tutorial

* Updating docs

* Updating gotm tutorial with figure

* Adding aquarium fabm0d tutorial

* Updates to docs

* Updating docs to include conda install

* Fixing GOTM version

.github/workflows/ersem.yml

@@ -1,6 +1,6 @@
 # This is a basic workflow to help you get started with Actions
 
-name: build-ersem
+name: ersem
 
 on:
   push:
@@ -9,40 +9,61 @@ on:
     branches: [ master ]
 
 jobs:
-  build-fabm-ersem:
+  build-pyfabm-ersem-debian:
     runs-on: ubuntu-latest
     steps:
-        - name: Checkout branch
-          uses: actions/checkout@v2
+        - uses: actions/checkout@v2
         - name: Setup python
           uses: actions/setup-python@v2
           with:
               python-version: '3.x'
-        - name: Installing wheel and numpy
-          run: python -m pip install wheel numpy
-        - name: Cloning FABM
-          run: git clone https://github.com/fabm-model/fabm.git
-        - name: Building FABM-ERSEM
+        - name: Installing PyFABM-ERSEM dependences
+          run: ./github-actions/pyfabm-ersem/pyfabm-ersem-dep-debian.sh
+        - name: Building and installing PyFABM-ERSEM
           run: |
-              mkdir build && cd build
-              cmake ../fabm/src/drivers/python -DFABM_ERSEM_BASE=..
-              make install
-        - name: Check installation
-          run: python -c "import fabm"
-  build-gotm-fabm-ersem:
+              branch=$(git branch --show-current)
+              ./github-actions/pyfabm-ersem/pyfabm-ersem-build.sh $branch
+        - name: Running pyfabm tutorial
+          run: |
+              python -m pip install matplotlib
+              python github-actions/pyfabm-ersem/pyfabm-tut.py
+  build-gotm-fabm-ersem-debian:
     runs-on: ubuntu-latest
     steps:
-        - name: Checkout branch
-          uses: actions/checkout@v2
-        - name: Installing netCDF
-          run: sudo apt-get install libnetcdff-dev
-        - name: Cloning FABM and GOTM
+        - uses: actions/checkout@v2
+        - name: Setup python
+          uses: actions/setup-python@v2
+          with:
+              python-version: '3.x'
+        - name: Installing GOTM-FABM-ERSEM dependences
+          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
+        - name: Building and installing GOTM-FABM-ERSEM
+          run: |
+              branch=$(git branch --show-current)
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh $branch
+        - name: Running tutorial
+          run: |
+              ./github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh
+              sudo apt install libnetcdff-dev
+              python -m pip install matplotlib netCDF4
+              python github-actions/gotm-fabm-ersem/gotm-tut.py -p ersem-setups/L4
+  build-fabm0d-gotm-ersem-debian:
+    runs-on: ubuntu-latest
+    steps:
+        - uses: actions/checkout@v2
+        - name: Setup python
+          uses: actions/setup-python@v2
+          with:
+              python-version: '3.x'
+        - name: Installing FABM0d-GOTM-ERSEM dependences
+          run: ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-dep-debian.sh
+        - name: Building and installing FABM0d-GOTM-ERSEM
           run: |
-              git clone https://github.com/fabm-model/fabm.git
-              git clone https://github.com/gotm-model/code.git gotm
-              cd gotm && git submodule update --init --recursive && cd ..
-        - name: Building GOTM-FABM-ERSEM
+              branch=$(git branch --show-current)
+              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh $branch
+        - name: Running tutorial
           run: |
-              mkdir build && cd build
-              cmake ../gotm -DFABM_BASE=../fabm -DFABM_ERSEM_BASE=..
-              make install
+              ./github-actions/fabm0d-gotm-ersem/aquarium-tut-config-setup.sh
+              sudo apt install libnetcdff-dev
+              python -m pip install matplotlib netCDF4
+              python github-actions/fabm0d-gotm-ersem/aquarium-tut.py -p ersem-setups/0d-aquarium/output.nc

.gitignore

@@ -0,0 +1,11 @@
+# Removing docs build
+docs/build/
+
+# Removing pycache
+__pycache__
+
+# the module index is built each time the docs
+docs/source/module_index.rst
+
+# removing swap files
+*.swp