Merge pull request #20 from cvxgrp/dev

Dev

.github/workflows/build.yml

@@ -11,20 +11,20 @@ jobs:
 
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
-              python-version: "3.9"
+              python-version: "3.10"
 
-          - name: Install Twine
-            run: sudo $pythonLocation/bin/python3 -m pip install twine wheel
+          - name: Install Twine and Build
+            run: sudo pip install twine build
 
           - name: Create the distribution
             run: |
               git fetch --prune --unshallow --tags
-              sudo $pythonLocation/bin/python3 setup.py sdist bdist_wheel
+              sudo python3 -m build
 
           - name: Publish package distributions to PyPI
             uses: pypa/gh-action-pypi-publish@release/v1
@@ -38,12 +38,12 @@ jobs:
             shell: bash -l {0}
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
-              python-version: "3.9"
+              python-version: "3.10"
 
           - name: Install Miniconda
             uses: conda-incubator/setup-miniconda@v2
@@ -52,28 +52,27 @@ jobs:
               activate-environment: ""
               miniconda-version: "latest"
 
-          - name: Install the Mamba Dependencies
-            run: | 
+          - name: Install the Conda Dependencies
+            run: |
               conda config --set always_yes yes --set auto_update_conda false
               conda update conda
-              conda install mamba -n base -c conda-forge
               conda install -n base conda-libmamba-solver
-              mamba install python=3.9 "conda-build=3.21" colorama pip ruamel ruamel.yaml rich mamba jsonschema -c conda-forge
-              $pythonLocation/bin/python3 -m pip install -e .
+              conda install python=3.10 conda-build colorama pip ruamel ruamel.yaml rich jsonschema -c conda-forge
+              git fetch --prune --unshallow --tags
+              pip install -e .
 
 # run install twice due to client-size to ensure all files downloaded
 # echo yes before login to prevent anaconda bug breaking automation
 # git tags MUST be fetched otherwise output will be blank
 # bash variables cannot be used in github actions, must use actions specific syntax and methods
           - name: Build the Anaconda Package
-            id: mambabuild
+            id: condabuild
             run: |
-              mamba install anaconda-client
-              conda config --set anaconda_upload no
+              conda install anaconda-client
+              conda config --set anaconda_upload no --set solver libmamba
               echo yes | anaconda login --username ${{ secrets.ANACONDA_CLOUD_USERNAME }} --password ${{ secrets.ANACONDA_CLOUD_PASSWORD }}
-              git fetch --prune --unshallow --tags
-              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c conda-forge -c stanfordcvxgrp --numpy 1.16.4
-              echo '::set-output name=gitversion::$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)'
+              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c anaconda -c conda-forge -c stanfordcvxgrp          
+              echo "gitversion=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)" >> $GITHUB_OUTPUT
 
           - name: Upload the Anaconda Package
             id: condaload

.github/workflows/test.yml

@@ -1,96 +1,99 @@
 name: Main Test
+
 on:
-    pull_request:
-    push:
-        branches:
-            - master
-        tags:
-          - '*'
+  push:
+  pull_request:
+    branches: [main]
+    types: [opened, reopened]
 jobs:
     run-tests:
         runs-on: ubuntu-latest
+        environment: test
+        strategy:
+          fail-fast: false
+          matrix:
+            python-version: [ "3.10", "3.11", "3.12" ]
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
-              python-version: '3.9'
+              python-version: ${{ matrix.python-version }}
 
-          - name: Install Dependencies
-            run: | 
-              sudo $pythonLocation/bin/python3 -m pip install -r requirements.txt
-              sudo $pythonLocation/bin/python3 -m pip install pytest
-              sudo $pythonLocation/bin/python3 -m pip install -e .
+          - name: Install Python Dependencies
+            run: |
+              curl -LsSf https://astral.sh/uv/install.sh | sh
+              uv pip install --system --break-system-packages -r requirements.txt
+              uv pip install --system --break-system-packages pytest pytest-cov pytest-github-report pytest-github-actions-annotate-failures
 
-# Current unit test is not consistent. Occasionally fails despite usually passing. Needs to be fixed.
           - name: Run Unit Tests
-            run: |
-              $pythonLocation/bin/python3 -m pytest --import-mode=append tests/
+            env:
+              pytest_github_report: true
+              pytest_verbosity: 2
+            run: pytest -v --cov=src --cov-report=xml --cov-report=term-missing --color=yes tests/
 
     test-build-pypi:
-        needs: run-tests
         runs-on: ubuntu-latest
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
-              python-version: "3.9"
+              python-version: "3.10"
 
-          - name: Install Twine
-            run: sudo $pythonLocation/bin/python3 -m pip install twine wheel
+          - name: Install Twine and Build
+            run: sudo pip install twine build
 
           - name: Create the distribution
             run: |
               git fetch --prune --unshallow --tags
-              sudo $pythonLocation/bin/python3 setup.py sdist bdist_wheel
+              sudo python3 -m build
 
     test-build-conda:
-        needs: run-tests
         runs-on: ubuntu-latest
 # sets default shell to remove need for source to run the conda shell
         defaults:
           run:
             shell: bash -l {0}
         steps:
           - name: Checkout Repository
-            uses: actions/checkout@v3
+            uses: actions/checkout@v4
 
           - name: Install Python
-            uses: actions/setup-python@v3
+            uses: actions/setup-python@v5
             with:
-              python-version: "3.9"
+              python-version: "3.10"
 
           - name: Install Miniconda
-            uses: conda-incubator/setup-miniconda@v2
+            uses: conda-incubator/setup-miniconda@v3
             with:
               auto-activate-base: true
               activate-environment: ""
               miniconda-version: "latest"
 
-          - name: Install the Mamba Dependencies
-            run: | 
+          - name: Install the Conda Dependencies
+            run: |
               conda config --set always_yes yes --set auto_update_conda false
               conda update conda
-              conda install mamba -n base -c conda-forge
               conda install -n base conda-libmamba-solver
-              mamba install python=3.9 "conda-build=3.21" colorama pip ruamel ruamel.yaml rich mamba jsonschema -c conda-forge
-              $pythonLocation/bin/python3 -m pip install -e .
+              conda install python=3.10 conda-build colorama pip ruamel ruamel.yaml rich jsonschema -c conda-forge
+              git fetch --prune --unshallow --tags
+              pip install -e .
 
 
 # run install twice due to client-size to ensure all files downloaded
 # echo yes before login to prevent anaconda bug breaking automation
 # git tags MUST be fetched otherwise output will be blank
 # bash variables cannot be used in github actions, must use actions specific syntax and methods
           - name: Build the Anaconda Package
-            id: mambabuild
+            id: condabuild
             run: |
-              mamba install anaconda-client
-              conda config --set anaconda_upload no
-              git fetch --prune --unshallow --tags
-              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c conda-forge -c stanfordcvxgrp --numpy 1.16.4
-              echo '::set-output name=gitversion::$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)'
+              conda install anaconda-client
+              conda clean --all
+              conda config --set anaconda_upload no --set solver libmamba
+              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)test conda build . -c conda-forge -c stanfordcvxgrp
+              echo "gitversion=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)" >> $GITHUB_OUTPUT

conda_recipe/meta.yaml

@@ -5,7 +5,7 @@ package:
   version: {{ environ.get('VERSION_FROM_GIT_TAG') }}
 
 source:
-  git_url: https://github.com/cvxgrp/signal-decomposition
+  path: .. # checked out repo instead of main repo branch
 
 build:
   noarch: python
@@ -15,32 +15,37 @@ build:
 requirements:
   host:
     - pip
-    - python >=3.9
-    - scipy
-    - numpy >=1.20
-    - scikit-learn
-    - cvxpy
-    - matplotlib
+    - python >=3.6
 
   run:
     - pip
     - python
     - scipy
-    - numpy >=1.20
+    - numpy
     - scikit-learn
     - cvxpy
     - matplotlib
+    - qss
+    - clarabel
+    - pandas
+
+test:
+  imports:
+    - gfosd
+  commands:
+    - pip check
+  requires:
+    - pip
 
 about:
   home: https://github.com/cvxgrp/signal-decomposition
-  license: BSD
+  license: BSD-3-Clause
+  license_file: LICENSE
   license_family: BSD
-  license_file:
-  summary: Optimzation-based signal decomposition
-  doc_url:
-  dev_url:
+  summary: Optimization-based signal decomposition
 
 extra:
   recipe-maintainers:
-    - Bennet Myers
-    - Thistleman
+    - bmeyers
+    - thistleman
+    - pluflou

gfosd/__init__.py

@@ -1 +1,2 @@
+from ._version import version as __version__
 from gfosd.problem import Problem

gfosd/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.2.dev30+gac101bd'
+__version_tuple__ = version_tuple = (0, 0, 2, 'dev30', 'gac101bd')

gfosd/components/__init__.py

@@ -2,9 +2,10 @@
                                    SumAbs,
                                    SumHuber,
                                    SumQuantile,
-                                   SumCard)
+                                   SumCard,
+                                   SumSquareReference)
 from gfosd.components.inequality_constraints import Inequality
-from gfosd.components.basis_constraints import Basis, Periodic
+from gfosd.components.basis_constraints import Basis, Periodic, Fourier
 from gfosd.components.finite_set import FiniteSet, Boolean
 from gfosd.components.aggregate import Aggregate
 from gfosd.components.equality_constraints import (FirstValEqual,

gfosd/components/aggregate.py

@@ -37,7 +37,10 @@ def prepare_attributes(self, T, p=1):
         self._Pz = sp.block_diag([
             c._Pz for c in self._gf_list
         ])
-        self._make_q()
+        # same logic as above but for q
+        qx = self._gf_list[g_ix]._q[:self._gf_list[g_ix].x_size]
+        qz = np.concatenate([c._q[self._gf_list[g_ix].x_size:] for c in self._gf_list])
+        self._q = np.concatenate([qx, qz])
         self._make_r()
         self._gx = self._make_gx()
         self._gz = self._make_gz()
@@ -53,6 +56,9 @@ def _make_P(self):
             c._Pz for c in self._gf_list
         ])
 
+    def _make_r(self):
+        self._r = np.sum([c._r for c in self._gf_list])
+
     def _make_gx(self):
         gx = []
         for ix, component in enumerate(self._gf_list):

gfosd/components/base_graph_class.py

@@ -94,10 +94,10 @@ def _make_P(self, size):
         return sp.dok_matrix(2 * (size,))
 
     def _make_q(self):
-        self._q = None
+        self._q = np.zeros(self.x_size + self.z_size)
 
     def _make_r(self):
-        self._r = None
+        self._r = 0
 
     def _make_g(self, size):
         return []