From 62679ecd4644ba42ab79648b6393e072a29391b2 Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Thu, 26 Mar 2026 14:39:51 +0100
Subject: [PATCH 01/11] replaced double array operation, switch mgrid for
 broadcast_to

---
 src/vip_hci/preproc/derotation.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/vip_hci/preproc/derotation.py b/src/vip_hci/preproc/derotation.py
index 83749f86..610c8ad6 100644
--- a/src/vip_hci/preproc/derotation.py
+++ b/src/vip_hci/preproc/derotation.py
@@ -219,7 +219,7 @@ def frame_rotate(array, angle, imlib='vip-fft', interpolation='lanczos4',
         array_prep = array.copy()
 
     # residual (non-interp) nans should be set to 0 to avoid bug in rotation
-    array_prep[np.where(np.isnan(array_prep))] = 0
+    array_prep[np.isnan(array_prep)] = 0
 
     y, x = array_prep.shape
 
@@ -604,9 +604,8 @@ def rotate_fft(array, angle):
     ori_y, ori_x = array_in.shape
 
     cy, cx = frame_center(array)
-    arr_xy = np.mgrid[0:ori_y, 0:ori_x]
-    arr_y = arr_xy[0]-cy
-    arr_x = arr_xy[1]-cx
+    arr_y = np.broadcast_to((np.arange(ori_y) - cy)[:, np.newaxis], (ori_y, ori_x))
+    arr_x = np.broadcast_to((np.arange(ori_x) - cx)[np.newaxis, :], (ori_y, ori_x))
 
     # TODO: make FFT padding work for other option than '0'.
     s_x = _fft_shear(array_in, arr_x, a, ax=1, pad=0)

From 83b95dc0da93b810e7085428e835dfb4f7891001 Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Thu, 26 Mar 2026 14:46:57 +0100
Subject: [PATCH 02/11] fix for no reference cube case in _adimsdi_doublepca

---
 src/vip_hci/psfsub/pca_fullfr.py | 48 +++++++++++++++++++++-----------
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/src/vip_hci/psfsub/pca_fullfr.py b/src/vip_hci/psfsub/pca_fullfr.py
index 877520e4..10dda4ae 100644
--- a/src/vip_hci/psfsub/pca_fullfr.py
+++ b/src/vip_hci/psfsub/pca_fullfr.py
@@ -1428,22 +1428,38 @@ def _adimsdi_doublepca(
             for frame in range(n):
                 ind = _find_indices_adi(angle_list, frame, pa_thr,
                                         truncate=truncate, max_frames=max_fr)
-
-                res_result = _project_subtract(
-                    res_cube_channels[:n],
-                    res_cube_channels[n:],
-                    ncomp_adi,
-                    scaling[1],
-                    mask_center_px,
-                    svd_mode,
-                    verbose,
-                    False,
-                    ind,
-                    frame,
-                    cube_sig=cube_sig,
-                    left_eigv=left_eigv,
-                    min_frames_pca=min_frames_pca,
-                )
+                if 'A' in ref_strategy or cube_ref is None:
+                    res_result = _project_subtract(
+                        res_cube_channels[:n],
+                        None,
+                        ncomp_adi,
+                        scaling[1],
+                        mask_center_px,
+                        svd_mode,
+                        verbose,
+                        False,
+                        ind,
+                        frame,
+                        cube_sig=cube_sig,
+                        left_eigv=left_eigv,
+                        min_frames_pca=min_frames_pca,
+                    )
+                else:
+                    res_result = _project_subtract(
+                        res_cube_channels[:n],
+                        res_cube_channels[n:],  # ref cube
+                        ncomp_adi,
+                        scaling[1],
+                        mask_center_px,
+                        svd_mode,
+                        verbose,
+                        False,
+                        ind,
+                        frame,
+                        cube_sig=cube_sig,
+                        left_eigv=left_eigv,
+                        min_frames_pca=min_frames_pca,
+                    )
                 res_ifs_adi[frame] = res_result[-1].reshape((y_in, x_in))
 
         if verbose:

From d0914b99c355f44e64cba33a03ca1aeaf7f75bbd Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Thu, 26 Mar 2026 15:08:48 +0100
Subject: [PATCH 03/11] bumping test versions before they get removed

---
 .github/workflows/ci.yml        | 12 ++++++------
 .github/workflows/draft-pdf.yml |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8892d946..63314428 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,9 +29,9 @@ jobs:
         group: [1, 2, 3]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -56,7 +56,7 @@ jobs:
         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@v3
+      uses: codecov/codecov-action@v5
 
   objects_check:
 
@@ -67,9 +67,9 @@ jobs:
         python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -93,4 +93,4 @@ jobs:
         coverage run --source=src/vip_hci/objects/ -m pytest tests/post_3_10
         coverage xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
index cce545f2..47ec13e3 100644
--- a/.github/workflows/draft-pdf.yml
+++ b/.github/workflows/draft-pdf.yml
@@ -6,7 +6,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:

From bbc593e9c09d747addfdd4f102c337afe7de5074 Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Thu, 26 Mar 2026 15:52:47 +0100
Subject: [PATCH 04/11] bumping actions to latest major version

---
 .github/workflows/ci.yml        | 12 ++++++------
 .github/workflows/draft-pdf.yml |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 63314428..20ba7ead 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,9 +29,9 @@ jobs:
         group: [1, 2, 3]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -56,7 +56,7 @@ jobs:
         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@v5
+      uses: codecov/codecov-action@v6
 
   objects_check:
 
@@ -67,9 +67,9 @@ jobs:
         python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -93,4 +93,4 @@ jobs:
         coverage run --source=src/vip_hci/objects/ -m pytest tests/post_3_10
         coverage xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
index 47ec13e3..6f6d14ea 100644
--- a/.github/workflows/draft-pdf.yml
+++ b/.github/workflows/draft-pdf.yml
@@ -6,7 +6,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
@@ -14,7 +14,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: paper.md
       - name: Upload
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

From 7f22dcb20c179d897eff026b04933f24c59c2e1b Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Fri, 27 Mar 2026 13:57:07 +0100
Subject: [PATCH 05/11] updating pre-commit hooks to v6

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 91a09a0e..3ba88f61 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

From 7e74a5c367db3745ce2219de369e70ffc7c2ead5 Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Fri, 27 Mar 2026 14:03:01 +0100
Subject: [PATCH 06/11] pre-commit runs once, drop unused code, cache pip

---
 .github/workflows/ci.yml | 45 +++++++++++++++-------------------------
 1 file changed, 17 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 20ba7ead..40e1309e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,4 +1,4 @@
-# This workflow will install Python depe:ndencies, run tests and lint with a variety of Python versions
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: ci
@@ -15,8 +15,20 @@ env:
   COVERAGE_CORE: sysmon
 
 jobs:
-  no_object_checks:
+  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 --all-files
 
+  no_object_checks:
+    needs: pre-commit
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -34,23 +46,11 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install --editable . --group dev
-    # Uncomment below when ready to deal with a lot of PEP8 formatting changes
-    - name: Verify files with pre-commit
-      run: |
-        # Setup pre-commit hooks
-        pre-commit clean
-        pre-commit autoupdate --repo https://github.com/pre-commit/pre-commit-hooks
-        pre-commit install --hook-type pre-merge-commit
-        pre-commit install --hook-type pre-push
-        pre-commit install --hook-type post-rewrite
-        pre-commit install-hooks
-        pre-commit install
-        # Run pre-commit hooks
-        pre-commit run --files src/**/*.py
     - name: Test with pytest
       run: |
         coverage run --source src -m pytest tests/pre_3_10 --splits 3 --group ${{ matrix.group }}
@@ -59,7 +59,7 @@ jobs:
       uses: codecov/codecov-action@v6
 
   objects_check:
-
+    needs: pre-commit
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -72,22 +72,11 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install --editable . --group dev
-    - name: Verify files with pre-commit
-      run: |
-        # Setup pre-commit hooks
-        pre-commit clean
-        pre-commit autoupdate --repo https://github.com/pre-commit/pre-commit-hooks
-        pre-commit install --hook-type pre-merge-commit
-        pre-commit install --hook-type pre-push
-        pre-commit install --hook-type post-rewrite
-        pre-commit install-hooks
-        pre-commit install
-        # Run pre-commit hooks
-        pre-commit run --files src/vip_hci/objects/*.py
     - name: Test with pytest
       run: |
         coverage run --source=src/vip_hci/objects/ -m pytest tests/post_3_10

From f28620bcb30731fc5ca915f35a4dcc18eb343bf6 Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Fri, 27 Mar 2026 14:18:04 +0100
Subject: [PATCH 07/11] pre-commit runs once, drop unused code, cache pip

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 40e1309e..ed31d85f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,7 +25,7 @@ jobs:
     - name: Run pre-commit
       run: |
         pip install pre-commit
-        pre-commit run --all-files
+        pre-commit run --files src/**/*.py
 
   no_object_checks:
     needs: pre-commit

From 2518f6f14d6fa9e58020676f7101c91a964f20aa Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Mon, 30 Mar 2026 12:11:33 +0200
Subject: [PATCH 08/11] bkg_proba can be imported

---
 src/vip_hci/stats/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/vip_hci/stats/__init__.py b/src/vip_hci/stats/__init__.py
index 4b6e7bd2..6ac11bc6 100644
--- a/src/vip_hci/stats/__init__.py
+++ b/src/vip_hci/stats/__init__.py
@@ -9,6 +9,7 @@
 - distance (correlation) between a cube and a reference frame.
 
 """
+from .bkg_proba import *
 from .clip_sigma import *
 from .distances import *
 from .im_stats import *

From 7897589a590c0f98ec1a2b75f985c367071faeea Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Mon, 30 Mar 2026 13:35:22 +0200
Subject: [PATCH 09/11] deleting unused files

---
 .travis.yml                                   | 20 -------------------
 ...thedocs_full_compilation_timeout_error.yml | 15 --------------
 2 files changed, 35 deletions(-)
 delete mode 100644 .travis.yml
 delete mode 100644 readthedocs_full_compilation_timeout_error.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 089dbffb..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-language: python
-
-sudo: required
-dist: xenial # no 3.7 on 14.04 Trusty
-
-python:
-  - 3.7
-  - 3.8
-  - 3.9
-
-# command to install dependencies
-install:
-  - pip install -e .
-
-# command to run tests + coverage
-script:
-  - pytest -v
-
-after_success:
-  - codecov
diff --git a/readthedocs_full_compilation_timeout_error.yml b/readthedocs_full_compilation_timeout_error.yml
deleted file mode 100644
index 0ca52ca0..00000000
--- a/readthedocs_full_compilation_timeout_error.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-# .readthedocs_timeout_error.yml
-
-version: 2
-
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.10"
-
-python:
-  install:
-    - requirements: docs/requirements.txt
-
-sphinx:
-  configuration: docs/source/conf.py

From b983edcdab32f8f2417a53f784ea83043c7e86f8 Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Mon, 30 Mar 2026 14:03:32 +0200
Subject: [PATCH 10/11] major fix to bkg_star_proba

---
 src/vip_hci/stats/bkg_proba.py | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/src/vip_hci/stats/bkg_proba.py b/src/vip_hci/stats/bkg_proba.py
index e4611d58..67970e36 100644
--- a/src/vip_hci/stats/bkg_proba.py
+++ b/src/vip_hci/stats/bkg_proba.py
@@ -11,9 +11,10 @@
 import numpy as np
 
 
-def bkg_star_proba(n_dens, sep, n_bkg=1, verbose=True, full_output=False):
+def bkg_star_proba(n_dens, sep, n_bkg=1, unit="deg", verbose=True,
+                   full_output=False):
     """ Given an input density of background star brighter than a certain
-    magnitude (obtained e.g. from the Besancon model or TRILEGAL), and the
+    magnitude (obtained e.g. from the Besançon model or TRILEGAL), and the
     separation of n_bkg point source, estimate the probability of having n_bkg
     or more background stars in a disk with radius equal to the largest
     separation.
@@ -23,12 +24,15 @@ def bkg_star_proba(n_dens, sep, n_bkg=1, verbose=True, full_output=False):
     ----------
     n_dens : float
         Number density of background stars in the direction of the object of
-        interest, in arcsec^-2.
+        interest. Units are set by the ``unit`` parameter.
     sep : float or numpy 1d array
         Separation of the point sources with respect to central star, in arcsec.
     n_bkg : int, opt
         Number of point sources in the field, and for which the separation is
         provided.
+    unit : str, opt
+        Unit of ``n_dens``. Either ``"deg"`` for deg^-2 (default, e.g. from
+        the Besançon model) or ``"arcsec"`` for arcsec^-2.
     verbose: bool, opt
         Whether to print the probabilities for 0 to n_bkg point sources.
     full_output: bool, opt
@@ -46,6 +50,11 @@ def bkg_star_proba(n_dens, sep, n_bkg=1, verbose=True, full_output=False):
     if n_bkg < 1 or not isinstance(n_bkg, int):
         raise TypeError("n_bkg should be a strictly positive integer.")
 
+    if unit == "deg":
+        n_dens = n_dens / 3600**2
+    elif unit != "arcsec":
+        raise ValueError("unit must be 'deg' or 'arcsec'.")
+
     if not isinstance(sep, float):
         if isinstance(sep, np.ndarray):
             if sep.ndim != 1 or sep.shape[0] != n_bkg:
@@ -61,14 +70,14 @@ def bkg_star_proba(n_dens, sep, n_bkg=1, verbose=True, full_output=False):
         probas[i] = np.exp(-n_dens*B)*(n_dens*B)**i/float(factorial(i))
         if verbose:
             msg = "Proba of having {:.0f} bkg star in a disk of "
-            msg += "{:.1}'' radius: {:.1f}%"
-            print(msg.format(i, sep, probas[i]))
+            msg += "{:.1}'' radius: {:.4g}%"
+            print(msg.format(i, sep, probas[i]*100))
 
     proba = 1-np.sum(probas)
     if verbose:
         msg = "Proba of having {:.0f} bkg star or more in a disk of "
-        msg += "{:.1}'' radius: {:.1f}%"
-        print(msg.format(n_bkg, sep, proba))
+        msg += "{:.1}'' radius: {:.4g}%"
+        print(msg.format(n_bkg, sep, proba*100))
 
     if full_output:
         return proba, probas

From f598105dfecdabc69127d46b782afacc222a2fbb Mon Sep 17 00:00:00 2001
From: IainHammond <dr.iain.hammond@gmail.com>
Date: Mon, 30 Mar 2026 14:13:34 +0200
Subject: [PATCH 11/11] major fix to bkg_star_proba

---
 src/vip_hci/stats/bkg_proba.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/vip_hci/stats/bkg_proba.py b/src/vip_hci/stats/bkg_proba.py
index 67970e36..968a9e6b 100644
--- a/src/vip_hci/stats/bkg_proba.py
+++ b/src/vip_hci/stats/bkg_proba.py
@@ -51,8 +51,13 @@ def bkg_star_proba(n_dens, sep, n_bkg=1, unit="deg", verbose=True,
         raise TypeError("n_bkg should be a strictly positive integer.")
 
     if unit == "deg":
+        if verbose:
+            print("Input n_dens unit: deg^-2")
         n_dens = n_dens / 3600**2
-    elif unit != "arcsec":
+    elif unit == "arcsec":
+        if verbose:
+            print("Input n_dens unit: arcsec^-2")
+    else:
         raise ValueError("unit must be 'deg' or 'arcsec'.")
 
     if not isinstance(sep, float):
@@ -70,13 +75,13 @@ def bkg_star_proba(n_dens, sep, n_bkg=1, unit="deg", verbose=True,
         probas[i] = np.exp(-n_dens*B)*(n_dens*B)**i/float(factorial(i))
         if verbose:
             msg = "Proba of having {:.0f} bkg star in a disk of "
-            msg += "{:.1}'' radius: {:.4g}%"
+            msg += "{:.2g}'' radius: {:.4g}%"
             print(msg.format(i, sep, probas[i]*100))
 
     proba = 1-np.sum(probas)
     if verbose:
         msg = "Proba of having {:.0f} bkg star or more in a disk of "
-        msg += "{:.1}'' radius: {:.4g}%"
+        msg += "{:.2g}'' radius: {:.4g}%"
         print(msg.format(n_bkg, sep, proba*100))
 
     if full_output: