From 1f54468e10cd87224188b0c11af1b4c358a51d3d Mon Sep 17 00:00:00 2001
From: lumbric <lumbric@gmail.com>
Date: Tue, 7 May 2024 18:31:38 +0200
Subject: [PATCH] Add dependencies and cleanup GH actions

---
 .github/workflows/dev.yml   |  63 ------
 .github/workflows/tests.yml |  42 ++++
 README.md                   |  17 +-
 env.yml                     | 368 ------------------------------------
 pyproject.toml              |  18 +-
 syfop/units.py              |   4 +
 6 files changed, 71 insertions(+), 441 deletions(-)
 delete mode 100644 .github/workflows/dev.yml
 create mode 100644 .github/workflows/tests.yml
 delete mode 100644 env.yml

diff --git a/.github/workflows/dev.yml b/.github/workflows/dev.yml
deleted file mode 100644
index d0cb85b..0000000
--- a/.github/workflows/dev.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-name: Dev build
-
-on: push
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-
-    # TODO need to check if this really works with conda that way
-    # strategy:
-    #   matrix:
-    #     python-versions: ['3.7', '3.8', '3.9', '3.10']
-
-    steps:
-      - name: Set up Git repository
-        uses: actions/checkout@v2
-
-      # Other Github actions to setup conda, not sure which is the best one:
-      #    https://github.com/marketplace/actions/setup-miniconda
-      #      --> seems to work fine
-      #    https://github.com/matthewrmshin/conda-action
-      #      --> No success, how to activate env? Has only 2 stars...
-      #    https://github.com/marketplace/actions/setup-conda
-      #      --> not tested yet
-      - name: Cache conda
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if env.yml has not changed
-          CACHE_NUMBER: 3
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('env.yml') }}
-
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          # python-version: 3.9
-          # mamba-version: "*"
-          # channels: conda-forge
-          # TODO might be a good idea, but does not work...
-          # channel-priority: strict
-          # use Mambaforge to avoid weird conda setup issue:
-          # https://github.com/conda-incubator/setup-miniconda/issues/116#issuecomment-1384648777
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: syfop
-          environment-file: env.yml
-          # TODO does this cause troubles with finding packages?
-          # https://github.com/conda-incubator/setup-miniconda/issues/267
-          # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-
-      - name: Lint wiht flake8 and black
-        shell: bash -l {0}
-        run: flake8 && black --check .
-
-      - name: Run unit tests (except the ones using Gurobi)
-        shell: bash -l {0}
-        run: python -m pytest --cov=. --cov-report=lcov -k "not gurobi and not cplex" tests
-
-      - name: Coveralls
-        uses: coverallsapp/github-action@master
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: coverage.lcov
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 0000000..5e84abe
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,42 @@
+name: Tests
+
+on: push
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    # strategy:
+    #   matrix:
+    #     python-versions: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+      - name: Set up Git repository
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          cache: 'pip' # caching pip dependencies
+
+      - name: Install syfop and dependencies
+        run: |
+          sudo apt-get install graphviz graphviz-dev  # for pygraphviz
+          python -m pip install --upgrade pip
+          python -m pip install -e .[dev,test,extra]
+
+      - name: Lint with flake8
+        run: flake8
+
+      - name: Lint with black
+        run: black --check .
+
+      - name: Run unit tests (except the ones using Gurobi and CPLEX)
+        shell: bash -l {0}
+        run: python -m pytest --cov=. --cov-report=lcov -k "not gurobi and not cplex" tests
+
+      - name: Coveralls test coverage
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: coverage.lcov
diff --git a/README.md b/README.md
index 7331ece..16f40b9 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 
 [![MIT License](https://img.shields.io/github/license/inwe-boku/syfop.svg)](https://choosealicense.com/licenses/mit/)
-[![CI](https://github.com/inwe-boku/syfop/actions/workflows/dev.yml/badge.svg)](https://github.com/inwe-boku/syfop/actions)
+[![CI](https://github.com/inwe-boku/syfop/actions/workflows/tests.yml/badge.svg)](https://github.com/inwe-boku/syfop/actions/workflows/tests.yml)
 [![Coverage Status](https://coveralls.io/repos/github/inwe-boku/syfop/badge.svg)](https://coveralls.io/github/inwe-boku/syfop)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![DOI](https://zenodo.org/badge/550867861.svg)](https://zenodo.org/doi/10.5281/zenodo.10869438)
@@ -40,16 +40,17 @@ see [demo.ipynb](notebooks/demo.ipynb)
 How to install
 --------------
 
-At the moment there is no package built for syfop. Use conda to setup an environment and then use
-`syfop` directly from a cloned Git repository:
+At the moment there is no package built for syfop, but it can be installed via pip directly from the
+repository:
 
-    git clone https://github.com/inwe-boku/syfop/
-    conda update -f env.yml
-    conda activate syfop
-    pre-commit install
+    pip install git+https://github.com/inwe-boku/syfop
+
+The solver HiGHs is installed automatically . Other [solvers](https://linopy.readthedocs.io/en/latest/solvers.html) are supported too, but not installed automatically.
 
+To install development requirements run:
 
-The conda environment contains the solver HiGHs. Other [solvers](https://linopy.readthedocs.io/en/latest/solvers.html) are supported too, but not included in the conda environment.
+    pip install -e 'syfop[test,dev] @ git+https://github.com/inwe-boku/syfop'
+    pre-commit install
 
 <!--
 To install Gurobiy:
diff --git a/env.yml b/env.yml
deleted file mode 100644
index 441fca6..0000000
--- a/env.yml
+++ /dev/null
@@ -1,368 +0,0 @@
-name: syfop
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - _ipython_minor_entry_point=8.7.0
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - accessible-pygments=0.0.4
-  - alabaster=0.7.16
-  - alsa-lib=1.2.8
-  - anyio=3.6.2
-  - appdirs=1.4.4
-  - argon2-cffi=21.3.0
-  - argon2-cffi-bindings=21.2.0
-  - arrow=1.3.0
-  - asttokens=2.2.1
-  - atk-1.0=2.38.0
-  - attr=2.5.1
-  - attrs=22.2.0
-  - babel=2.14.0
-  - backcall=0.2.0
-  - backports=1.1
-  - backports.functools_lru_cache=1.6.4
-  - beautifulsoup4=4.11.1
-  - black=22.12.0
-  - blas=1.0
-  - bleach=5.0.1
-  - bokeh=2.4.3
-  - bottleneck=1.3.5
-  - brotli=1.0.9
-  - brotli-bin=1.0.9
-  - brotlipy=0.7.0
-  - bzip2=1.0.8
-  - c-ares=1.18.1
-  - ca-certificates=2022.12.7
-  - cached-property=1.5.2
-  - cached_property=1.5.2
-  - cairo=1.16.0
-  - certifi=2022.12.7
-  - cffi=1.15.1
-  - cftime=1.6.2
-  - charset-normalizer=2.1.1
-  - click=8.1.3
-  - cloudpickle=2.2.0
-  - colorama=0.4.6
-  - comm=0.1.2
-  - contourpy=1.0.7
-  - coverage=7.0.5
-  - cryptography=39.0.0
-  - curl=7.87.0
-  - cycler=0.11.0
-  - cytoolz=0.12.0
-  - dask=2023.1.0
-  - dask-core=2023.1.0
-  - dbus=1.13.18
-  - debugpy=1.6.5
-  - decorator=5.1.1
-  - defusedxml=0.7.1
-  - deprecation=2.1.0
-  - distributed=2023.1.0
-  - docutils=0.20.1
-  - entrypoints=0.4
-  - exceptiongroup=1.1.0
-  - executing=1.2.0
-  - expat=2.5.0
-  - fftw=3.3.10
-  - flake8=6.0.0
-  - flit-core=3.8.0
-  - font-ttf-dejavu-sans-mono=2.37
-  - font-ttf-inconsolata=3.000
-  - font-ttf-source-code-pro=2.038
-  - font-ttf-ubuntu=0.83
-  - fontconfig=2.14.1
-  - fonts-conda-ecosystem=1
-  - fonts-conda-forge=1
-  - fonttools=4.38.0
-  - fqdn=1.5.1
-  - freetype=2.12.1
-  - fribidi=1.0.10
-  - fsspec=2022.11.0
-  - gdk-pixbuf=2.42.10
-  - gettext=0.21.1
-  - giflib=5.2.1
-  - gitdb=4.0.11
-  - gitpython=3.1.42
-  - glib=2.74.1
-  - glib-tools=2.74.1
-  - graphite2=1.3.13
-  - graphviz=6.0.2
-  - gst-plugins-base=1.21.3
-  - gstreamer=1.21.3
-  - gstreamer-orc=0.4.33
-  - gtk2=2.24.33
-  - gts=0.7.6
-  - harfbuzz=6.0.0
-  - hdf4=4.2.15
-  - hdf5=1.12.2
-  - heapdict=1.0.1
-  - icu=70.1
-  - idna=3.4
-  - imagesize=1.4.1
-  - importlib-metadata=6.0.0
-  - importlib_metadata=6.0.0
-  - importlib_resources=5.10.2
-  - iniconfig=2.0.0
-  - ipdb=0.13.13
-  - ipykernel=6.20.2
-  - ipython=8.7.0
-  - ipython_genutils=0.2.0
-  - ipywidgets=8.0.4
-  - isoduration=20.11.0
-  - jack=1.9.21
-  - jedi=0.18.2
-  - jinja2=3.1.2
-  - jpeg=9e
-  - jsonpointer=2.4
-  - jsonschema=4.17.3
-  - jsonschema-with-format-nongpl=4.17.3
-  - jupyter=1.0.0
-  - jupyter-server-mathjax=0.2.6
-  - jupyter_client=7.4.9
-  - jupyter_console=6.4.4
-  - jupyter_core=5.1.3
-  - jupyter_events=0.6.3
-  - jupyter_server=2.1.0
-  - jupyter_server_terminals=0.4.4
-  - jupyterlab_pygments=0.2.2
-  - jupyterlab_widgets=3.0.5
-  - keyutils=1.6.1
-  - kiwisolver=1.4.4
-  - krb5=1.20.1
-  - lame=3.100
-  - lcms2=2.14
-  - ld_impl_linux-64=2.39
-  - lerc=4.0.0
-  - libaec=1.0.6
-  - libblas=3.9.0
-  - libbrotlicommon=1.0.9
-  - libbrotlidec=1.0.9
-  - libbrotlienc=1.0.9
-  - libcap=2.66
-  - libcblas=3.9.0
-  - libclang=15.0.7
-  - libclang13=15.0.7
-  - libcups=2.3.3
-  - libcurl=7.87.0
-  - libdb=6.2.32
-  - libdeflate=1.17
-  - libedit=3.1.20221030
-  - libev=4.33
-  - libevent=2.1.10
-  - libexpat=2.5.0
-  - libffi=3.4.2
-  - libflac=1.4.2
-  - libgcc-ng=12.2.0
-  - libgcrypt=1.10.1
-  - libgd=2.3.3
-  - libgfortran-ng=12.2.0
-  - libgfortran5=12.2.0
-  - libglib=2.74.1
-  - libgomp=12.2.0
-  - libgpg-error=1.46
-  - libiconv=1.17
-  - libjpeg-turbo=2.1.4
-  - liblapack=3.9.0
-  - libllvm15=15.0.7
-  - libnetcdf=4.8.1
-  - libnghttp2=1.51.0
-  - libnsl=2.0.0
-  - libogg=1.3.5
-  - libopenblas=0.3.21
-  - libopus=1.3.1
-  - libpng=1.6.39
-  - libpq=15.1
-  - librsvg=2.54.4
-  - libsndfile=1.2.0
-  - libsodium=1.0.18
-  - libsqlite=3.40.0
-  - libssh2=1.10.0
-  - libstdcxx-ng=12.2.0
-  - libsystemd0=252
-  - libtiff=4.5.0
-  - libtool=2.4.7
-  - libudev1=252
-  - libuuid=2.32.1
-  - libvorbis=1.3.7
-  - libwebp=1.2.4
-  - libwebp-base=1.2.4
-  - libxcb=1.13
-  - libxkbcommon=1.0.3
-  - libxml2=2.10.3
-  - libzip=1.9.2
-  - libzlib=1.2.13
-  - linopy=0.3.8
-  - locket=1.0.0
-  - lz4=4.2.0
-  - lz4-c=1.9.4
-  - markupsafe=2.1.1
-  - matplotlib=3.6.2
-  - matplotlib-base=3.6.2
-  - matplotlib-inline=0.1.6
-  - mccabe=0.7.0
-  - mistune=2.0.4
-  - mpg123=1.31.2
-  - msgpack-python=1.0.4
-  - munkres=1.1.4
-  - mypy_extensions=0.4.3
-  - mysql-common=8.0.31
-  - mysql-libs=8.0.31
-  - nbclassic=0.4.8
-  - nbclient=0.7.2
-  - nbconvert=7.2.8
-  - nbconvert-core=7.2.8
-  - nbconvert-pandoc=7.2.8
-  - nbdime=4.0.1
-  - nbformat=5.7.3
-  - ncurses=6.3
-  - nest-asyncio=1.5.6
-  - netcdf4=1.6.2
-  - networkx=3.0
-  - nomkl=3.0
-  - notebook=6.5.2
-  - notebook-shim=0.2.2
-  - nspr=4.35
-  - nss=3.82
-  - numexpr=2.8.4
-  - numpy=1.24.1
-  - openblas=0.3.21
-  - openjpeg=2.5.0
-  - openssl=3.0.7
-  - packaging=23.0
-  - pandas=1.5.2
-  - pandoc=2.19.2
-  - pandocfilters=1.5.0
-  - pango=1.50.12
-  - parso=0.8.3
-  - partd=1.3.0
-  - patchelf=0.17.2
-  - pathspec=0.10.3
-  - pcre2=10.40
-  - pexpect=4.8.0
-  - pickleshare=0.7.5
-  - pillow=9.4.0
-  - pip=24.0
-  - pixman=0.40.0
-  - pkgutil-resolve-name=1.3.10
-  - platformdirs=2.6.2
-  - pluggy=1.0.0
-  - ply=3.11
-  - pooch=1.6.0
-  - prometheus_client=0.15.0
-  - prompt-toolkit=3.0.36
-  - prompt_toolkit=3.0.36
-  - psutil=5.9.4
-  - pthread-stubs=0.4
-  - ptyprocess=0.7.0
-  - pulseaudio=16.1
-  - pure_eval=0.2.2
-  - py=1.11.0
-  - pycodestyle=2.10.0
-  - pycparser=2.21
-  - pydata-sphinx-theme=0.15.2
-  - pydot=1.4.2
-  - pyflakes=3.0.1
-  - pygments=2.14.0
-  - pygraphviz=1.10
-  - pyopenssl=23.0.0
-  - pyparsing=3.0.9
-  - pyqt=5.15.7
-  - pyqt5-sip=12.11.0
-  - pyrsistent=0.19.3
-  - pysocks=1.7.1
-  - pytest=7.2.1
-  - pytest-cov=4.0.0
-  - python=3.10.8
-  - python-dateutil=2.8.2
-  - python-fastjsonschema=2.16.2
-  - python-json-logger=2.0.4
-  - python_abi=3.10
-  - pytz=2022.7.1
-  - pyyaml=6.0.1
-  - pyzmq=25.0.0
-  - qt-main=5.15.6
-  - qtconsole=5.4.0
-  - qtconsole-base=5.4.0
-  - qtpy=2.3.0
-  - readline=8.2
-  - requests=2.28.2
-  - rfc3339-validator=0.1.4
-  - rfc3986-validator=0.1.1
-  - scipy=1.10.0
-  - send2trash=1.8.0
-  - setuptools=66.0.0
-  - sip=6.7.5
-  - six=1.16.0
-  - smmap=5.0.0
-  - sniffio=1.3.0
-  - snowballstemmer=2.2.0
-  - sortedcontainers=2.4.0
-  - soupsieve=2.3.2.post1
-  - sphinx=7.2.6
-  - sphinx-book-theme=1.1.2
-  - sphinxcontrib-applehelp=1.0.8
-  - sphinxcontrib-devhelp=1.0.6
-  - sphinxcontrib-htmlhelp=2.0.5
-  - sphinxcontrib-jsmath=1.0.1
-  - sphinxcontrib-qthelp=1.0.7
-  - sphinxcontrib-serializinghtml=1.1.10
-  - sqlite=3.40.0
-  - stack_data=0.6.2
-  - tblib=1.7.0
-  - terminado=0.17.1
-  - tinycss2=1.2.1
-  - tk=8.6.12
-  - toml=0.10.2
-  - tomli=2.0.1
-  - toolz=0.12.0
-  - tornado=6.2
-  - tqdm=4.64.1
-  - traitlets=5.8.1
-  - types-python-dateutil=2.8.19.20240106
-  - typing-extensions=4.4.0
-  - typing_extensions=4.4.0
-  - tzdata=2022g
-  - unicodedata2=15.0.0
-  - uri-template=1.3.0
-  - urllib3=1.26.14
-  - wcwidth=0.2.6
-  - webcolors=1.13
-  - webencodings=0.5.1
-  - websocket-client=1.4.2
-  - wheel=0.38.4
-  - widgetsnbextension=4.0.5
-  - xarray=2024.2.0
-  - xcb-util=0.4.0
-  - xcb-util-image=0.4.0
-  - xcb-util-keysyms=0.4.0
-  - xcb-util-renderutil=0.3.9
-  - xcb-util-wm=0.4.1
-  - xorg-kbproto=1.0.7
-  - xorg-libice=1.0.10
-  - xorg-libsm=1.2.3
-  - xorg-libx11=1.7.2
-  - xorg-libxau=1.0.9
-  - xorg-libxdmcp=1.1.3
-  - xorg-libxext=1.3.4
-  - xorg-libxrender=0.9.10
-  - xorg-renderproto=0.11.1
-  - xorg-xextproto=7.3.0
-  - xorg-xproto=7.0.31
-  - xz=5.2.8
-  - yaml=0.2.5
-  - zeromq=4.3.4
-  - zict=2.2.0
-  - zipp=3.11.0
-  - zlib=1.2.13
-  - zstd=1.5.2
-  - pip:
-    - cplex==22.1.1.0
-    - docplex==2.25.236
-    - grandalf==0.8
-    - highspy==1.1.2.dev3
-    - netgraph==4.11.7
-    - pybind11==2.10.1
-    - pyomo==6.4.3
-    - rectangle-packer==2.0.1
-    - sphinxawesome-theme==5.1.1
diff --git a/pyproject.toml b/pyproject.toml
index 0aa1c2e..8575983 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,23 +17,37 @@ dependencies = [
     "pandas >= 1.5",    # no idea which version is really necessary
     "linopy == 0.3.8",  # might work also with newer versions, but they break APIs often
     "pint",             # used for units
+    "pint-xarray",      # used for units for xarray objects
+    "highspy",
     "networkx",
     "netgraph",         # optional dependency for plotting
 ]
 
 [project.optional-dependencies]
-# TODO not sure if this is complete
+# optional dependencies
+extra = [
+    "graphviz",
+    "pygraphviz",
+]
+
+# for development
 dev = [
   "pre-commit",
   "black",
   "isort",
   "flake8",
-  "flake8-docstrings",
+  # "flake8-docstrings",  # this is too strict ATM but would be nice to add
 ]
+
+# for running tests
 test = [
   "pytest",
   "pytest-cov"
 ]
+# for building the documentation
+doc = [
+  # TODO
+]
 
 [tool.setuptools]
 packages = ["syfop"]
diff --git a/syfop/units.py b/syfop/units.py
index 5d333df..eb2eac4 100644
--- a/syfop/units.py
+++ b/syfop/units.py
@@ -18,6 +18,10 @@
     "gas": ureg.MW,
     "methanol": ureg.t / ureg.h,
     # TODO heat? coal?
+    # TODO this should be moved to unit tests as soon as we have a way to add user defined units
+    "milk": ureg.l / ureg.h,
+    "cacao": ureg.g / ureg.h,
+    "hot_chocolate": ureg.l / ureg.h,
 }