Swap to pdm (#166)

* Swap to pdm
* Use quivr's drop_duplicates
* Upgrade adam_core >= 0.2.5

.github/workflows/conda-build-lint-test.yml

@@ -16,6 +16,8 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    env:
+      OORB_DATA: /tmp/oorb/data
 
     steps:
       - name: Checkout git repo
@@ -28,24 +30,16 @@ jobs:
           activate-environment: "thor"
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies (excluding adam_core and quivr since they are not available via conda)
+      - name: Install openorb dependencies
         run: |
-          tail +3 requirements.txt > requirements_conda.txt
-          conda install -c defaults -c conda-forge -c astropy -c moeyensj --file requirements_conda.txt --yes
-      - name: Update OBSCODE.dat
-        run: |
-          cd $CONDA_PREFIX/share/oorb
-          curl https://www.minorplanetcenter.net/iau/lists/ObsCodes.html -o ObsCodes.html
-          sed -e '2d' ObsCodes.html | grep -v "<" > OBSCODE.dat
-          rm -f ObsCodes.html
-          cp OBSCODE.dat $CONDA_PREFIX/share/openorb/OBSCODE.dat
-      - name: Install adam_core and quivr
-        run: |
-          pip install adam-core@git+https://github.com/B612-Asteroid-Institute/adam_core@main
-          pip install quivr@git+https://github.com/moeyensj/quivr@concatenate-empty-attributes
+          sudo apt-get update -y
+          sudo apt-get install -y gfortran liblapack-dev
+          wget  -P /tmp/ https://storage.googleapis.com/oorb-data/oorb_data.tar.gz
+          mkdir -p /tmp/oorb/
+          tar -xvf /tmp/oorb_data.tar.gz -C /tmp/oorb/
       - name: Build and install
-        run: pip install . --no-deps
+        run: pip install .[dev]
       - name: Lint
-        run: pre-commit run --all-files
+        run: pdm lint
       - name: Test
-        run: pytest . --cov
+        run: pdm test

.github/workflows/docker-build-lint-test.yml

@@ -1,4 +1,3 @@
-
 name: docker - Build Lint and Test
 
 on:
@@ -12,16 +11,18 @@ jobs:
     runs-on: ubuntu-latest
     env:
       IMAGE_TAG: ${{ github.sha }}
+      OORB_DATA: /tmp/oorb/data
+
     steps:
       - name: Checkout git repo
         uses: actions/checkout@v4
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
         with:
           install: true
       - name: Build
         run: docker build --load -t thor:$IMAGE_TAG .
       - name: Lint
-        run: docker run -i thor:$IMAGE_TAG pre-commit run --all-files
+        run: docker run -i thor:$IMAGE_TAG pdm lint
       - name: Test
-        run: docker run -i thor:$IMAGE_TAG pytest . --cov
+        run: docker run -i thor:$IMAGE_TAG pdm test

.github/workflows/pip-build-integration-test.yml

@@ -15,29 +15,28 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    env:
+      OORB_DATA: /tmp/oorb/data
 
     steps:
       - name: Checkout git repo
         uses: actions/checkout@v4
       - name: Get git tags
         run:  git fetch --prune --unshallow --tags
-      - name: Set up miniconda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: "thor"
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Install openorb using conda
-        run: conda install -c defaults -c conda-forge openorb --yes
-      - name: Update OBSCODE.dat
-        run: |
-          cd $CONDA_PREFIX/share/oorb && ./updateOBSCODE
-          cp OBSCODE.dat $CONDA_PREFIX/share/openorb/OBSCODE.dat
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip' # caching pip dependencies
-      - name: Build and install
-        run: pip install .[tests]
+      - name: Install openorb dependencies
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y gfortran liblapack-dev
+          wget  -P /tmp/ https://storage.googleapis.com/oorb-data/oorb_data.tar.gz
+          mkdir -p /tmp/oorb/
+          tar -xvf /tmp/oorb_data.tar.gz -C /tmp/oorb/
+      - name: Install Dependencies
+        run: |
+          pip install pip --upgrade
+          pip install ".[dev]"
       - name: Integration Tests
-        run: pytest . -m "integration"
+        run: pdm test -k integration

.github/workflows/pip-build-lint-test-coverage.yml

@@ -16,38 +16,36 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    env:
+      OORB_DATA: /tmp/oorb/data
 
     steps:
       - name: Checkout git repo
         uses: actions/checkout@v4
       - name: Get git tags
         run:  git fetch --prune --unshallow --tags
-      - name: Set up miniconda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: "thor"
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Install openorb using conda
-        run: conda install -c defaults -c conda-forge openorb --yes
-      - name: Update OBSCODE.dat
-        run: |
-          cd $CONDA_PREFIX/share/oorb
-          curl https://www.minorplanetcenter.net/iau/lists/ObsCodes.html -o ObsCodes.html
-          sed -e '2d' ObsCodes.html | grep -v "<" > OBSCODE.dat
-          rm -f ObsCodes.html
-          cp OBSCODE.dat $CONDA_PREFIX/share/openorb/OBSCODE.dat
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip' # caching pip dependencies
-      - name: Build and install
-        run: pip install .[tests]
+      - name: Install openorb dependencies
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y gfortran liblapack-dev
+          wget  -P /tmp/ https://storage.googleapis.com/oorb-data/oorb_data.tar.gz
+          mkdir -p /tmp/oorb/
+          tar -xvf /tmp/oorb_data.tar.gz -C /tmp/oorb/
+      - name: Install Dependencies
+        run: |
+          pip install pip --upgrade
+          pip install ".[dev]"
       - name: Lint
-        run: pre-commit run --all-files
-      - name: Test
-        run: pytest . --cov --cov-report xml
-      - name: Coverage
+        run: pdm run lint
+      # - name: Type check
+      #   run: pdm run typecheck
+      - name: Test with coverage
+        run: pdm run coverage
+      - name: Coverage Report
         uses: coverallsapp/[email protected]
         with:
           github-token: ${{ secrets.COVERALLS_TOKEN }}

.gitignore

@@ -1,7 +1,5 @@
-# Data files
-thor/data
-thor/data/log.yaml
-thor/version.py
+# Version file: set by pdm-scm
+src/thor/_version.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -108,7 +106,7 @@ ipython_config.py
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
+pdm.lock
 #   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
 #   in version control.
 #   https://pdm.fming.dev/#use-with-ide

Dockerfile

@@ -1,56 +1,22 @@
-FROM ubuntu:latest
+FROM python:3.11
 
 # Set shell to bash
 SHELL ["/bin/bash", "-c"]
+CMD ["/bin/bash"]
 
 # Update system dependencies
 RUN apt-get update \
     && apt-get upgrade -y \
-    && apt-get install -y curl gfortran git liblapack-dev make pip python3.11 python-is-python3 unzip wget
+    && apt-get install -y pip git wget tar gfortran liblapack-dev
 
-# Upgrade pip to the latest version and install pre-commit
-RUN pip install --upgrade pip pre-commit
-RUN pip install --upgrade cython==0.29.36 setuptools setuptools_scm
-RUN chmod 777 /opt
-
-# Install numpy
-RUN git clone https://github.com/numpy/numpy.git /opt/numpy
-RUN cd /opt/numpy && git checkout v1.24.4 && git submodule update --init
-RUN cd /opt/numpy && python3 setup.py build --cpu-baseline=native install
-
-
-# Install openorb
-# TODO: We need a more robust way to be appropriately natively compiled pyoorb installed
-# including data file generation
-RUN git clone https://github.com/B612-Asteroid-Institute/oorb.git /opt/oorb
-RUN cd /opt/oorb && git checkout fork
-RUN cd /opt/oorb && ./configure gfortran opt --with-pyoorb --with-f2py=/usr/local/bin/f2py --with-python=python3
-# Add '-march=native' to compiler options by running a sed
-# script directly on the Makefile.includse file. This is a
-# hack to get around the fact that the configure script
-# doesn't support this option.
-RUN sed -i 's/FCOPTIONS = .*/FCOPTIONS = $(FCOPTIONS_OPT_GFORTRAN) -march=native/g' /opt/oorb/Makefile.include
-# --no-build-isolation is needed because we need to ensure we use
-# the same version of numpy as the one we compiled previously so
-# that it matches the version of f2py we passed in to ./configure.
-RUN pip install --no-build-isolation -v /opt/oorb
-
-# Generate the data files
-RUN cd /opt/oorb && make ephem
-RUN cd /opt/oorb/data && ./getBC430
-RUN cd /opt/oorb/data && ./updateOBSCODE
-ENV OORBROOT=/opt/oorb
-ENV OORB_DATA=/opt/oorb/data
-
-# Install pre-commit hooks (before THOR is installed to cache this step)
-RUN mkdir /code/
-COPY .pre-commit-config.yaml /code/
-WORKDIR /code/
-RUN git init . \
-    && git add .pre-commit-config.yaml \
-    && pre-commit install-hooks \
-    && rm -rf .git
+# Install openorb dependencies
+RUN wget -P /tmp/ https://storage.googleapis.com/oorb-data/oorb_data.tar.gz \
+    && mkdir -p /tmp/oorb/ \
+    && tar -xvf /tmp/oorb_data.tar.gz -C /tmp/oorb/
+ENV OORB_DATA=/tmp/oorb/data/
 
 # Install THOR
+RUN mkdir -p /code/
+WORKDIR /code/
 ADD . /code/
-RUN SETUPTOOLS_SCM_PRETEND_VERSION=1 pip install -e .[tests,dev]
+RUN pip install -e .[dev]

MANIFEST.in

@@ -1,4 +1,4 @@
-include thor/*.py
+include src/*.py
 include *.md
 include *.toml
 include *.yaml