Merge pull request #32 from ecmwf/fix/simplify_dependencies

corentincarton · web-flow · commit 53a8c137aba1 · 2024-08-15T15:42:15.000+01:00
Fix/simplify dependencies
diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -7,37 +7,29 @@ on:
     branches: [ "main", "develop" ]
 
 jobs:
-  
+
   quality_assurance:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - run: pip install black flake8 isort
-      - run: isort --check .
-      - run: black --check .
-      - run: flake8 .
-  
+      - run: pip install ruff
+      - run: ruff check
+
   docs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - run: pip install -r docs/requirements.txt
       - run: mkdocs build
-  
+
   setup_and_test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          activate-environment: test
-          environment-file: environment.yml
-          auto-activate-base: false
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v2
       - name: install hat package
         shell: bash -l {0}
-        run: pip install .
+        run: pip install .[test]
       - name: run tests
         shell: bash -l {0}
-        run: |
-          pip install pytest
-          pytest
+        run: pytest
diff --git a/.github/workflows/on-push.yml b/.github/workflows/on-push.yml
@@ -23,40 +23,41 @@ jobs:
     name: setup
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: actions/setup-python@v2
-      - run: python -m pip install .
+      - name: install hat package
+        shell: bash -l {0}
+        run: pip install .
 
   test:
     name: test
     runs-on: ubuntu-latest
+    needs: [setup]
     steps:
-      - uses: actions/checkout@v2
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          activate-environment: test
-          environment-file: environment.yml
-          auto-activate-base: false
-      - name: install hat package
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v2
+      - name: developer install of hat package
         shell: bash -l {0}
-        run: pip install .
+        run: pip install .[test]
       - name: run tests
         shell: bash -l {0}
-        run: |
-          pip install pytest
-          pytest
+        run: pytest
 
   distribution:
+    name: distribution
     runs-on: ubuntu-latest
-    needs: [setup, test]
-
+    needs: [setup]
     steps:
     - uses: actions/checkout@v3
-    - name: Build distributions
+    - uses: actions/setup-python@v2
+    - name: install hat package
+      shell: bash -l {0}
+      run: pip install .
+    - name: build distributions
       run: |
-        $CONDA/bin/python -m pip install build
-        $CONDA/bin/python -m build
-    - name: Publish a Python distribution to PyPI
+        pip install build
+        python build
+    - name: publish a Python distribution to PyPI
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,13 +1,31 @@
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
 repos:
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-#  - repo: https://github.com/PyCQA/flake8
-#    rev: 6.0.0
-#    hooks:
-#      - id: flake8
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.5.6
+      hooks:
+          - id: ruff
+            args: [ --fix ]
+          - id: ruff-format
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: detect-private-key
+          - id: check-ast
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+          - id: check-case-conflict
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'
diff --git a/README.md b/README.md
@@ -1,10 +1,12 @@
 # HAT - Hydrological Analysis Toolkit
 
-HAT is a suite of tools to perform data analysis on hydrological datasets.
+The Hydrological Analysis Toolkit (HAT) is a software suite for hydrologists working with simulated and observed river discharge. HAT performs data analysis on hydrological datasets, with its main features being:
+- mapping station locations into hydrological model grids
+- extraction of timeseries
+- statistical analysis of hydrological timeseries
 
 The documentation can be found at https://hydro-analysis-toolkit.readthedocs.io
 
-
 **DISCLAIMER**
 This project is **BETA** and will be **Experimental** for the foreseeable future.
 Interfaces and functionality are likely to change, and the project itself may be scrapped.
@@ -15,28 +17,53 @@ Interfaces and functionality are likely to change, and the project itself may be
 Clone source code repository
 
     $ git clone https://github.com/ecmwf/hat.git
+    $ cd hat
 
-Create conda python environment
+Create and activate conda environment
+
+    $ conda env create -n hat python=3.10
+    $ conda activate hat
+
+For default installation, run
 
-    $ cd hat
-    $ conda env create -f environment.yml
     $ pip install .
 
-### Usage
+For a developer installation (includes linting and test libraries), run
 
-Start a hat environment
+    $ pip install .[dev]
+    $ pre-commit install
+
+If you only plan to run the tests, instead run
+
+    $ pip install .[test]
+
+If you plan to build a source and a wheel distribution, it is additionally required to run
+
+    $ pip install build
+
+### Usage
 
-    $ conda activate hat
-    
 Run a command line tool
 
     $ hat-extract-timeseries --help
 
+### Running the tests
+
+Tests are stored in the `tests/` folder and can be run with
+
+    $ pytest
+
+### Deployment
+
+To build a source and a wheel distribution, run
+
+    $ python build
+
 ### Contributing
 
-The main repository is hosted on [GitHub](https://github.com/ecmwf/hat), testing, bug reports and contributions are highly welcomed and appreciated.
+The main repository is hosted on [GitHub](https://github.com/ecmwf/hat). Testing, bug reports and contributions are highly welcomed and appreciated.
 
-Please report [bug](https://github.com/ecmwf/hat/issues) reports or [pull-requests](https://github.com/ecmwf/hat/pulls) on [GitHub](https://github.com/ecmwf/hat)
+Please report [bug](https://github.com/ecmwf/hat/issues) reports or [pull-requests](https://github.com/ecmwf/hat/pulls) on [GitHub](https://github.com/ecmwf/hat).
 
 We want your feedback, please e-mail: user-services@ecmwf.int
 
diff --git a/docs/index.md b/docs/index.md
@@ -1,3 +1,6 @@
 # Welcome to HAT
 
-Hydrological Analysis Tools (HAT) is a suite of software for hydrologists working with simulated and observed river discharge.
+The Hydrological Analysis Toolkit (HAT) is a software suite for hydrologists working with simulated and observed river discharge. HAT performs data analysis on hydrological datasets, with its main features being:
+- mapping station locations into hydrological model grids
+- extraction of timeseries
+- statistical analysis of hydrological timeseries
diff --git a/docs/installation.md b/docs/installation.md
@@ -2,20 +2,16 @@
 
 Clone source code repository
 
-    git clone git@github.com:ecmwf-projects/hat.git
+    git clone https://github.com/ecmwf/hat.git
+    cd hat
 
 Create conda python environment
 
-    cd hat
-
     # If on HPC..
     # module load conda
-
-    conda env create -f environment.yml
+    conda env create -n hat python=3.10
     conda activate hat
 
-Install HAT software
+Installation of required dependencies
 
     pip install .
-
-Open a new terminal to start
diff --git a/docs/usage.md b/docs/usage.md
@@ -2,7 +2,7 @@
 
 If you have already [installed](installation.md) hat then
 
-#### Activate environment
+#### Activate Environment
 
     $ conda activate hat
 
@@ -21,4 +21,3 @@ In your python code you can import the hat module
     import hat
 
 For examples, please see these [jupyter notebooks](https://github.com/ecmwf-projects/hat/tree/main/notebooks)
-
diff --git a/environment.yml b/environment.yml
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: Hydrological Analysis Tools
+site_name: Hydrological Analysis Toolkit
 site_url: https://ecmwf.github.io/hat/
 
 nav:
@@ -10,4 +10,4 @@ nav:
         - hat-extract-timeseries: hat_extract-timeseries.md
         - hat-hydrostats: hat_hydrostats.md
 
-theme: readthedocs
+theme: readthedocs
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,3 @@
-
 [build-system]
 requires = ["setuptools>=65", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
@@ -40,7 +39,12 @@ dependencies = [
     "ipyleaflet",
     "ipywidgets",
     "earthkit-data",
-    "cfgrib"
+    "cfgrib",
+    "netCDF4",
+    "eccodes",
+    "plotly",
+    "jupyter",
+    "geopy"
 ]
 
 [project.urls]
@@ -50,25 +54,27 @@ dependencies = [
 
 [project.optional-dependencies]
     test = [
-        "pytest",
+        "pytest"
     ]
-    docs = [
-        "mkdocs",
-        "mkdocs-material",
-        "mkdocstrings-python",
-        "mkdocs-autorefs",
-        "mkdocs-gen-files",
-        "pymdown-extensions",
-        "markdown-exec[ansi]",
+    dev = [
+        "pytest",
+        "ruff",
+        "pre-commit"
     ]
 
 [project.scripts]
     hat-extract-timeseries = "hat.tools.extract_simulation_timeseries_cli:main"
     hat-hydrostats = "hat.tools.hydrostats_cli:main"
     hat-stations-mapping = "hat.mapping.station_mapping:main"
 
-[tool.isort]
-profile="black"
+# Linting settings
+[tool.ruff]
+line-length = 120
+indent-width = 4
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
 
 # Testing
 [tool.pytest]
@@ -98,4 +104,4 @@ write_to_template = '''
 __version__ = "{version}"
 '''
 parentdir_prefix_version='hat-'  # get version from GitHub-like tarballs
-fallback_version='0.7.1'
+fallback_version='0.7.1'
