137 setuptools is not installing requirements properly (#138)

* shift from setuptools to poetry
* add poetry.lock
* remove python from env and manage by poetry instead
* windows pip test. ubuntu poetry test. auto version from init
* update README

.github/workflows/build-and-test.yml

@@ -0,0 +1,39 @@
+name: Build and test
+
+on: [push, pull_request]
+
+jobs:
+  Windows_pip:
+    runs-on: windows-latest
+    timeout-minutes: 60
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v2
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install pyopia
+        run: pip install ./
+
+      - name: Test
+        run: python -m pytest -v
+  Ubuntu_poetry:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10' 
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+      - name: Install dependencies
+        run: poetry install
+      - name: Run the automated tests
+        run: poetry run pytest -v

README.md

@@ -81,38 +81,29 @@ cd pyopia-main
 
 For the next steps, you need to be located in the directory that contains the file 'environment.yml'.
 
-2. Create a virtual environment using the environment.yml (will create an environment called pyopia):
+1. (optional, but recommended) Create a virtual environment using the environment.yml. This will create an environment called pyopia, but with no dependencies installed. Dependencies are managed by poetry (in step 2):
 
 ```bash
 conda env create -f environment.yml
 ```
-
-3. To update, we recommend a forced re-install:
-
-```bash
-conda env create -f environment.yml --force
-```
-
-(but you could also try this, which might be quicker but a less reliable form of updating):
+and activate the environment:
 
 ```bash
-conda env update --file environment.yml --prune
+conda activate pyopia
 ```
 
-4. To activate:
+2. Install dependencies using poetry:
 
 ```bash
-conda activate pyopia
+poetry install
 ```
 
-5. Test that it works with:
+3. (optional) Run local tests:
 
 ```bash
-python setup.py develop
+poetry run pytest
 ```
 
-Note that `pip install` or `python setup.py install` will probably cause you problems if you want to develop the code, and should only be used for deployment purposes.
-
 ----
 # License
 

docs/requirements.txt

@@ -1,12 +1,12 @@
-    flake8
-    docopt
-    setuptools
-    pytest-error-for-skips
-    sphinx_rtd_theme>=0.5.0
-    sphinxcontrib-napoleon>=0.7
-    sphinx-togglebutton
-    sphinx-copybutton
-    readthedocs-sphinx-search
-    myst-nb
-    jupyter_book
-    ipykernel>=6.19.4
+flake8
+docopt
+setuptools
+pytest-error-for-skips
+sphinx_rtd_theme>=0.5.0
+sphinxcontrib-napoleon>=0.7
+sphinx-togglebutton
+sphinx-copybutton
+readthedocs-sphinx-search
+myst-nb
+jupyter_book
+ipykernel>=6.19.4

environment.yml

@@ -2,5 +2,4 @@ name: pyopia
 channels:
     - conda-forge
 dependencies:
-    - python=3.10
-    - pip
+    - poetry

pyproject.toml

@@ -1,4 +1,51 @@
+[tool.poetry]
+name = "pyopia"
+version = "0"
+description = "A Python Ocean Particle Image Analysis toolbox."
+authors = ["Emlyn Davies <emlyn.davies@sintef.no>"]
+readme = "README.md"
+packages = [{include = "pyopia"}]
+
+[tool.poetry.dependencies]
+python = ">=3.10,<3.12"
+flake8 = "^6.1.0"
+numpy = "^1.24.0"
+pandas = {version = ">=2.1", extras = ["computation", "hdf5"]}
+h5py = "^3.9.0"
+scipy = "^1.11.2"
+scikit-image = "^0.21.0"
+pytest = ">=7.2.0"
+imageio = "^2.31.3"
+matplotlib = ">=3.7"
+tqdm = "^4.66.1"
+pytest-error-for-skips = "^2.0.2"
+nbclient = "0.7"
+sphinx = "5.0"
+sphinx-rtd-theme = ">=0.5.0"
+sphinxcontrib-napoleon = ">=0.7"
+sphinx-togglebutton = "^0.3.2"
+sphinx-copybutton = "^0.5.2"
+readthedocs-sphinx-search = "^0.3.1"
+myst-nb = "^0.17.2"
+jupyter-book = "^0.15.1"
+ipykernel = ">=6.19.4"
+urllib3 = "<2.0"
+gdown = "^4.7.1"
+cmocean = "^3.0.3"
+toml = "^0.10.2"
+xarray = "^2023.8.0"
+typer = {extras = ["all"], version = "^0.9.0"}
+tensorflow-io-gcs-filesystem = "0.31.0"
+tensorflow-cpu = "^2.13.0"
+
+[tool.poetry-version-plugin]
+source = "init"
+
+[tool.poetry.scripts]
+pyopia = "pyopia.cli:app"
+
 [build-system]
-requires = ["setuptools", "setuptools-scm"]
-build-backend = "setuptools.build_meta"
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
 
+[tool.setuptools_scm]