Few major bug fixes + improvements to the test suite

.github/workflows/ci.yml

@@ -18,45 +18,89 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
-    - uses: actions/setup-python@v6
-      with:
-        python-version: "3.14"
-    - name: Run pre-commit
-      run: |
-        pip install pre-commit
-        pre-commit run --files src/**/*.py
+      - uses: actions/checkout@main
+      - uses: actions/setup-python@main
+        with:
+          python-version: "3.14"
+          cache: pip
+      - name: Run pre-commit
+        run: |
+          pip install pre-commit
+          pre-commit run --files $(git ls-files "*.py")
 
   no_object_checks:
     needs: pre-commit
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version:
-          - "3.11"
-          - "3.12"
-          - "3.13"
-          - "3.14"
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         group: [1, 2, 3]
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@main
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install --editable . --group dev
-    - name: Test with pytest
+
+    - name: Test with pytest + coverage
+      if: matrix.python-version == '3.14'
       run: |
-        coverage run --source src -m pytest tests/pre_3_10 --splits 3 --group ${{ matrix.group }}
-        coverage xml
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v6
+        coverage run --source src --parallel-mode -m pytest tests/pre_3_10 --splits 3 --group ${{ matrix.group }}
+
+    - name: Test with pytest
+      if: matrix.python-version != '3.14'
+      run: pytest tests/pre_3_10 --splits 3 --group ${{ matrix.group }}
+
+    # upload each coverage shard file for combining later
+    - name: Upload coverage shard
+      if: matrix.python-version == '3.14'
+      uses: actions/upload-artifact@main
+      with:
+        name: coverage-no-objects-group-${{ matrix.group }}
+        path: .coverage.*
+        include-hidden-files: true
+
+  # combine the three shards before uploading to codecov
+  coverage_no_objects:
+    needs: no_object_checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@main
+
+      - uses: actions/setup-python@main
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install --editable . --group dev
+
+      - name: Download coverage shards
+        uses: actions/download-artifact@main
+        with:
+          pattern: coverage-no-objects-group-*
+          merge-multiple: true
+
+      - name: Combine and export coverage
+        run: |
+          coverage combine
+          coverage xml
+
+      - name: Upload to Codecov
+        uses: codecov/codecov-action@main
+        with:
+          flags: no_objects  # distinguishes this suite in the Codecov UI
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   objects_check:
     needs: pre-commit
@@ -67,19 +111,31 @@ jobs:
         python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@main
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install --editable . --group dev
-    - name: Test with pytest
+
+    - name: Test with pytest + coverage
+      if: matrix.python-version == '3.14'
       run: |
         coverage run --source=src/vip_hci/objects/ -m pytest tests/post_3_10
         coverage xml
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v6
+
+    - name: Test with pytest
+      if: matrix.python-version != '3.14'
+      run: pytest tests/post_3_10
+
+    - name: Upload to Codecov
+      if: matrix.python-version == '3.14'
+      uses: codecov/codecov-action@main
+      with:
+        flags: objects
+        token: ${{ secrets.CODECOV_TOKEN }}

Makefile

@@ -56,7 +56,7 @@ test:
 	pre-commit install-hooks
 	pre-commit install
 	pre-commit run --files src/**/*.py
-	coverate run -m pytest
+	coverage run -m pytest
 	coverage xml
 	rm confi_hist.pdf
 	rm confi_hist_gaussfit.pdf

helpers/update_docs_rst_from_README.py

@@ -6,14 +6,14 @@
 
 with open("../README.rst") as f_r:
     readme = f_r.readlines()
-str_titles = ['TL;DR', 
+str_titles = ['TL;DR',
               'Installation and dependencies',
               'Image conventions',
               'Contact',
               'Attribution',
               'THE END']
 titles_occ = [0,0,0,1,0,0]
-w_titles = ['TLDR', 
+w_titles = ['TLDR',
             'Installation-and-dependencies',
             'Image-conventions',
             'Contact',
@@ -37,6 +37,6 @@
                 stop_write=True
             else:
                 continue
-            
-            
+
+
 print("successfully converted README into documentation rst files.")

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=42", "wheel"]
+requires = ["setuptools>=64"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -26,7 +26,6 @@ classifiers = [
   "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering :: Astronomy",
 ]
-urls.Homepage = "https://github.com/vortex-exoplanet/VIP"
 dependencies = [
     "astropy>=5.0.0",
     "corner>=2.2.1",
@@ -45,6 +44,10 @@ dependencies = [
     "scikit-learn>=1.0.2",
 ]
 
+[project.urls]
+Homepage = "https://github.com/vortex-exoplanet/VIP"
+Issues = "https://github.com/vortex-exoplanet/VIP/issues"
+
 [dependency-groups]
 dev = [
     "coverage>=7.10.0",
@@ -67,3 +70,13 @@ dev = [
     "sphinx_rtd_theme",
     "jupyter_sphinx",
 ]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"vip_hci" = ["py.typed"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-v --tb=short"

src/vip_hci/config/paramenum.py

@@ -316,13 +316,13 @@ class OptMethod(str, Enum):
 
     * ``LSQ``
 
-    * ``ROBUST``
+    * ``L1``
     """
 
     NO = "no"
     TOTAL = "total"
     LSQ = "lsq"
-    ROBUST = "robust"
+    L1 = "l1"
 
 
 class VarEstim(str, Enum):

src/vip_hci/fm/fakecomp.py

@@ -97,7 +97,7 @@ def cube_inject_companions(array, psf_template, angle_list, flevel, rad_dists,
         Number of CPUs to use for multiprocessing. If None, will be
         automatically set to half the number of available CPUs.
     copy_array: bool, optional
-        Default is True. If False, ``array`` is not copied before injection. This is intended for 
+        Default is True. If False, ``array`` is not copied before injection. This is intended for
         computing performance when ``array`` can be modified.
 
     Returns

src/vip_hci/fm/fakedisk.py

@@ -61,6 +61,7 @@ def cube_inject_fakedisk(
     """
     if not fakedisk.ndim == 2:
         raise TypeError("Fakedisk is not a frame or a 2d array.")
+    angle_list = np.asarray(angle_list)
     if not angle_list.ndim == 1:
         raise TypeError("Input parallactic angle is not a 1d array")
 

src/vip_hci/fm/negfc_fmerit.py

@@ -251,7 +251,7 @@ def chisquare(
         imlib=imlib_sh,
         interpolation=interpolation,
         transmission=transmission,
-        radial_gradient=radial_gradient, 
+        radial_gradient=radial_gradient,
         verbose=False
     )
 

src/vip_hci/greedy/ipca_fullfr.py

@@ -146,20 +146,20 @@ def ipca(*all_args: List, **all_kwargs: dict):
         but has no additional options for the extraction of circumstellar signal
         at each iteration (all signals > 0 are considered). Installation of the
         GreeDS package is required for this option.
-        - If 'Christiaens24': Same as 'Juillard23' but not in Torch, and with 
+        - If 'Christiaens24': Same as 'Juillard23' but not in Torch, and with
         the extra parameters ``thr`` and ``ncomp_step`` available.
     ncomp : int or tuple/list of 2 or 3 int, optional
         How many PCs are used as a lower-dimensional subspace to project the
         target frames.
         - if mode is None:
             * strategy in {'ADI', 'RDI', 'ARDI'} and no ``mask_rdi`` provided:
             an int must be provided, ``ncomp`` is the fixed number of PCs to use
-            
+
             * strategy in {'RADI' , 'RARDI'} and no ``mask_rdi`` is provided:
             an int or a tuple/list of 2 int is accepted. In the latter case, the
             first value is used for IPCA-RDI, and the second for IPCA-ADI for
             the remaining iterations after the former converged.
-            
+
             * strategy in {'ADI', 'RDI', 'ARDI} and ``mask_rdi`` is provided: an
             int or a tuple/list of 2 int can be provided. In the latter case,
             the first value is used for PCA-data imputation at the first
@@ -170,12 +170,12 @@ def ipca(*all_args: List, **all_kwargs: dict):
             the first value is used for PCA-data imputation at the first
             iteration, the second for IPCA-RDI，and the third for IPCA-ADI for
             the remaining iterations after the former converged.
-            
+
          - if mode is not None:
              ncomp should correspond to the maximum number of principal
              components to be tested. The first ncomp will be ``ncomp_start``
              and the increment will be ``ncomp_step``.
-             
+
     ncomp_start: int, opt
         For incremental versions of iterative PCA (i.e. if mode is 'Juillard23'
         or 'Christiaens24'), this is the number of principal components at the
@@ -188,10 +188,10 @@ def ipca(*all_args: List, **all_kwargs: dict):
         Number of iterations for the iterative PCA.
         - if mode is None:
             total number of iterations
-            
+
         - if mode is 'Juillard23', or 'Christiaens24':
             iterations per tested ncomp.
-            
+
     strategy: str {'ADI, 'RDI', 'ARDI', 'RADI', 'RARDI''}, opt
         Whether to do iterative ADI only ('ADI'), iterative RDI only ('RDI'),
         iterative ADI and RDI together ('ARDI', i.e. with a combined PCA
@@ -201,7 +201,7 @@ def ipca(*all_args: List, **all_kwargs: dict):
         'ARDI', 'RADI' and 'RARDI'.
     thr: float or 'auto', opt
         Minimum threshold used to identify significant signals in the PCA image
-        obtained at each iteration, according to ``thr_mode``. 
+        obtained at each iteration, according to ``thr_mode``.
     thr_mode: str {'STIM', 'abs'}, opt
         How the threshold is expressed: whether based on the STIM map ('STIM')
         or expressed as absolute pixel intensity threshold ('abs'). The optimal
@@ -615,9 +615,9 @@ def _blurring_3d(array, mask_center_sz, fwhm_sz=2):
         pca_params['ncomp'] = final_ncomp[0]
         pca_params['cube'] = cube_tmp
         pca_params['cube_ref'] = cube_ref_tmp
-        
+
         res = pca(**pca_params, **rot_options)
-        
+
         frame = res[0]
         residuals_cube = res[-2]
         residuals_cube_ = res[-1]

src/vip_hci/invprob/andromeda.py

@@ -134,7 +134,7 @@ def andromeda(*all_args: List, **all_kwargs: dict):
         by ``roa * annuli_width``.
         ``roa`` is forced to ``1`` when ``opt_method="no"`` is chosen.
         IDL parameter: ``RATIO_OPT_AREA_INPUT``
-    opt_method : {'no', 'total', 'lsq', 'robust'}, optional
+    opt_method : {'no', 'total', 'lsq', 'l1'}, optional
         Method used to balance for the flux difference that exists between the
         two subtracted annuli in an optimal way during ADI.
         IDL parameter: ``OPT_METHOD_ANG_INPUT``

src/vip_hci/invprob/utils_andro.py

@@ -8,6 +8,7 @@
 
 
 import numpy as np
+from astropy.stats import median_absolute_deviation
 
 
 def robust_std(x):
@@ -32,8 +33,8 @@ def robust_std(x):
     based on ``LibAndromeda/robust_stddev.pro`` v1.1 2016/02/16
 
     """
-    median_absolute_deviation = np.median(np.abs(x - np.median(x)))
-    return median_absolute_deviation / 0.6745
+    mad = median_absolute_deviation(x)
+    return mad / 0.6745
 
 
 def idl_round(x):
@@ -84,7 +85,7 @@ def idl_where(array_expression):
       returns ``[]``, which is more "pythonic".
 
     """
-    res = np.array([i for i, e in enumerate(array_expression.flatten()) if e])
+    res = np.flatnonzero(array_expression)
     return res
 
 
@@ -285,7 +286,7 @@ def calc_psf_shift_subpix(psf, precision):
 
     """
     n = psf.shape[0]
-    psf_cube = np.zeros((precision+1, precision+1, n, n))
+    psf_cube = np.empty((precision+1, precision+1, n, n))
 
     for i_column in range(precision+1):
         decalx = i_column/precision