Fix various issues

.github/workflows/ci.yml

@@ -36,4 +36,4 @@ jobs:
       run: |
         pytest --cov=vip_hci/ --cov-report=xml --splits 3 --group ${{ matrix.group }}
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3

docs/source/vip_hci.psfsub.rst

@@ -68,6 +68,14 @@ vip\_hci.psfsub.pca\_local module
    :undoc-members:
    :show-inheritance:
 
+vip\_hci.psfsub.pca\_return\_utils module
+-----------------------------------------
+
+.. automodule:: vip_hci.psfsub.pca_return_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 vip\_hci.psfsub.svd module
 --------------------------
 

docs/source/vip_hci.var.rst

@@ -36,6 +36,22 @@ vip\_hci.var.iuwt module
    :undoc-members:
    :show-inheritance:
 
+vip\_hci.var.object\_utils module
+---------------------------------
+
+.. automodule:: vip_hci.var.object_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+vip\_hci.var.paramenum module
+-----------------------------
+
+.. automodule:: vip_hci.var.paramenum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 vip\_hci.var.shapes module
 --------------------------
 

requirements-dev.txt

@@ -4,10 +4,11 @@ sphinx
 pandoc
 pytest
 pytest-cov ~=2.6.0
-codecov ~=2.0.15
 pytest-split
 flake8
 flake8-bandit
 flake8-docstrings
 autopep8
 sphinx-rtd-theme
+StrEnum
+ratelimit

tests/conftest.py

@@ -2,14 +2,14 @@
 Configuration file for pytest, containing global ("session-level") fixtures.
 
 """
-import time
 import copy
+import time
 
 import numpy as np
 import pytest
-from astropy.utils.data import download_file
 
 import vip_hci as vip
+from .helpers import download_resource
 
 
 @pytest.fixture(scope="session")
@@ -23,17 +23,19 @@ def example_dataset_adi():
 
     Notes
     -----
-    Astropy's ``download_file`` uses caching, so the file is downloaded at most
-    once per test run.
+    We use the helper function ``download_resource`` which handles the request
+    and puts it to sleep for a defined duration if too many requests are done.
+    They inherently call the Astropy's ``download_file`` function which uses caching,
+    so the file is downloaded at most once per test run.
 
     """
     print("downloading data...")
 
     url_prefix = "https://github.com/vortex-exoplanet/VIP_extras/raw/master/datasets"
 
-    f1 = download_file("{}/naco_betapic_cube_cen.fits".format(url_prefix), cache=True)
-    f2 = download_file("{}/naco_betapic_psf.fits".format(url_prefix), cache=True)
-    f3 = download_file("{}/naco_betapic_pa.fits".format(url_prefix), cache=True)
+    f1 = download_resource("{}/naco_betapic_cube_cen.fits".format(url_prefix))
+    f2 = download_resource("{}/naco_betapic_psf.fits".format(url_prefix))
+    f3 = download_resource("{}/naco_betapic_pa.fits".format(url_prefix))
 
     # load fits
     cube = vip.fits.open_fits(f1)
@@ -89,18 +91,20 @@ def example_dataset_ifs():
 
     Notes
     -----
-    Astropy's ``download_file`` uses caching, so the file is downloaded at most
-    once per test run.
+    We use the helper function ``download_resource`` which handles the request
+    and puts it to sleep for a defined duration if too many requests are done.
+    They inherently call the Astropy's ``download_file`` function which uses caching,
+    so the file is downloaded at most once per test run.
 
     """
     print("downloading data...")
 
     url_prefix = "https://github.com/vortex-exoplanet/VIP_extras/raw/master/datasets"
 
-    f1 = download_file("{}/sphere_v471tau_cube.fits".format(url_prefix), cache=True)
-    f2 = download_file("{}/sphere_v471tau_psf.fits".format(url_prefix), cache=True)
-    f3 = download_file("{}/sphere_v471tau_pa.fits".format(url_prefix), cache=True)
-    f4 = download_file("{}/sphere_v471tau_wl.fits".format(url_prefix), cache=True)
+    f1 = download_resource("{}/sphere_v471tau_cube.fits".format(url_prefix))
+    f2 = download_resource("{}/sphere_v471tau_psf.fits".format(url_prefix))
+    f3 = download_resource("{}/sphere_v471tau_pa.fits".format(url_prefix))
+    f4 = download_resource("{}/sphere_v471tau_wl.fits".format(url_prefix))
 
     # load fits
     cube = vip.fits.open_fits(f1)
@@ -139,18 +143,20 @@ def example_dataset_ifs_crop():
 
     Notes
     -----
-    Astropy's ``download_file`` uses caching, so the file is downloaded at most
-    once per test run.
+    We use the helper function ``download_resource`` which handles the request
+    and puts it to sleep for a defined duration if too many requests are done.
+    They inherently call the Astropy's ``download_file`` function which uses caching,
+    so the file is downloaded at most once per test run.
 
     """
     print("downloading data...")
 
     url_prefix = "https://github.com/vortex-exoplanet/VIP_extras/raw/master/datasets"
 
-    f1 = download_file("{}/sphere_v471tau_cube.fits".format(url_prefix), cache=True)
-    f2 = download_file("{}/sphere_v471tau_psf.fits".format(url_prefix), cache=True)
-    f3 = download_file("{}/sphere_v471tau_pa.fits".format(url_prefix), cache=True)
-    f4 = download_file("{}/sphere_v471tau_wl.fits".format(url_prefix), cache=True)
+    f1 = download_resource("{}/sphere_v471tau_cube.fits".format(url_prefix))
+    f2 = download_resource("{}/sphere_v471tau_psf.fits".format(url_prefix))
+    f3 = download_resource("{}/sphere_v471tau_pa.fits".format(url_prefix))
+    f4 = download_resource("{}/sphere_v471tau_wl.fits".format(url_prefix))
 
     # load fits
     cube = vip.fits.open_fits(f1)
@@ -191,17 +197,19 @@ def example_dataset_rdi():
 
     Notes
     -----
-    Astropy's ``download_file`` uses caching, so the file is downloaded at most
-    once per test run.
+    We use the helper function ``download_resource`` which handles the request
+    and puts it to sleep for a defined duration if too many requests are done.
+    They inherently call the Astropy's ``download_file`` function which uses caching,
+    so the file is downloaded at most once per test run.
 
     """
     print("downloading data...")
 
     url_prefix = "https://github.com/vortex-exoplanet/VIP_extras/raw/master/datasets"
 
-    f1 = download_file("{}/naco_betapic_cube_cen.fits".format(url_prefix), cache=True)
-    f2 = download_file("{}/naco_betapic_psf.fits".format(url_prefix), cache=True)
-    f3 = download_file("{}/naco_betapic_pa.fits".format(url_prefix), cache=True)
+    f1 = download_resource("{}/naco_betapic_cube_cen.fits".format(url_prefix))
+    f2 = download_resource("{}/naco_betapic_psf.fits".format(url_prefix))
+    f3 = download_resource("{}/naco_betapic_pa.fits".format(url_prefix))
 
     # load fits
     cube = vip.fits.open_fits(f1)

tests/helpers.py

@@ -4,10 +4,12 @@
 
 __author__ = "Thomas Bédrine, Ralf Farkas"
 
-__all__ = ["check_detection"]
+__all__ = ["check_detection", "download_resource"]
 
 import pytest
 from pytest import mark, param, raises, fixture
+from ratelimit import limits, sleep_and_retry
+from astropy.utils.data import download_file
 import vip_hci as vip
 import numpy as np
 
@@ -76,3 +78,9 @@ def verify_expcoord(vectory, vectorx, exp_yx):
     )
     msg = "Injected companion not recovered"
     assert verify_expcoord(table.y, table.x, yx_exp), msg
+
+
+@sleep_and_retry
+@limits(calls=1, period=1)
+def download_resource(url):
+    return download_file(url, cache=True)

tests/snapshots/snapshot_invprob.py

@@ -13,6 +13,7 @@
 from vip_hci.fits import open_fits
 from vip_hci.objects import Dataset
 from vip_hci.config import VLT_NACO
+from tests.helpers import download_resource
 
 INVADI_PATH = "./tests/snapshots/invprob_adi/"
 DATASET_ELEMENTS = ["cube", "angles", "psf"]
@@ -28,17 +29,19 @@ def make_dataset_adi():
 
     Notes
     -----
-    Astropy's ``download_file`` uses caching, so the file is downloaded at most
-    once per test run.
+    We use the helper function ``download_resource`` which handles the request
+    and puts it to sleep for a defined duration if too many requests are done.
+    They inherently call the Astropy's ``download_file`` function which uses caching,
+    so the file is downloaded at most once per test run.
 
     """
     print("downloading data...")
 
     url_prefix = "https://github.com/vortex-exoplanet/VIP_extras/raw/master/datasets"
 
-    f1 = download_file(f"{url_prefix}/naco_betapic_cube_cen.fits", cache=True)
-    f2 = download_file(f"{url_prefix}/naco_betapic_psf.fits", cache=True)
-    f3 = download_file(f"{url_prefix}/naco_betapic_pa.fits", cache=True)
+    f1 = download_resource(f"{url_prefix}/naco_betapic_cube_cen.fits")
+    f2 = download_resource(f"{url_prefix}/naco_betapic_psf.fits")
+    f3 = download_resource(f"{url_prefix}/naco_betapic_pa.fits")
 
     # load fits
     cube = open_fits(f1)

tests/snapshots/snapshot_psfsub.py

@@ -9,10 +9,10 @@
 import numpy as np
 from vip_hci.psfsub import median_sub, frame_diff, llsg, xloci, nmf, nmf_annular
 from vip_hci.metrics import detection, snrmap
-from astropy.utils.data import download_file
 from vip_hci.fits import open_fits
 from vip_hci.objects import Dataset
 from vip_hci.config import VLT_NACO
+from tests.helpers import download_resource
 
 PSFADI_PATH = "./tests/snapshots/psfsub_adi/"
 DATASET_ELEMENTS = ["cube", "angles", "psf"]
@@ -28,17 +28,19 @@ def make_dataset_adi():
 
     Notes
     -----
-    Astropy's ``download_file`` uses caching, so the file is downloaded at most
-    once per test run.
+    We use the helper function ``download_resource`` which handles the request
+    and puts it to sleep for a defined duration if too many requests are done.
+    They inherently call the Astropy's ``download_file`` function which uses caching,
+    so the file is downloaded at most once per test run.
 
     """
     print("downloading data...")
 
     url_prefix = "https://github.com/vortex-exoplanet/VIP_extras/raw/master/datasets"
 
-    f1 = download_file(f"{url_prefix}/naco_betapic_cube_cen.fits", cache=True)
-    f2 = download_file(f"{url_prefix}/naco_betapic_psf.fits", cache=True)
-    f3 = download_file(f"{url_prefix}/naco_betapic_pa.fits", cache=True)
+    f1 = download_resource(f"{url_prefix}/naco_betapic_cube_cen.fits")
+    f2 = download_resource(f"{url_prefix}/naco_betapic_psf.fits")
+    f3 = download_resource(f"{url_prefix}/naco_betapic_pa.fits")
 
     # load fits
     cube = open_fits(f1)

tests/test_objects_ppnmf.py

@@ -43,7 +43,7 @@ def test_nmf_object(injected_cube_position):
     """
     Compare detections obtained through procedural and object versions of NMF.
 
-    Generate a frame with ``vip_hci.objects.ppmediansub`` and ensure its detection match
+    Generate a frame with ``vip_hci.objects.ppnmf`` and ensure its detection match
     with its procedural counterpart. This is done by getting the snapshot of the
     ``vip_hci.psfsub.nmf`` function, generated preemptively with
     ``tests.snapshots.save_snapshots_psfsub``. Also done with