Merge branch 'master' into relax_scipy_pin

CHANGES.rst

@@ -1,6 +1,23 @@
 1.12.6 (unreleased)
 ===================
 
+background
+----------
+
+- Ensure that WFSS background mask does not leave only
+  pixels with DO_NOT_USE flagged. [#8070]
+
+documentation
+-------------
+
+- Remove the CRDS PUB notices througout the documentation [#8075]
+
+extract_1d
+----------
+
+- Include zero values in dispersion direction check during
+  SOSS ATOCA algorithm [#8038]
+
 general
 -------
 
@@ -22,6 +39,11 @@ imprint
 - Updated the logging to report which imprint image is being subtracted from the
   science image. [#8041]
 
+ramp_fitting
+------------
+
+- Moving some ramp fitting CI tests from JWST to STCAL. [#8060]
+
 resample
 --------
 
@@ -36,6 +58,19 @@ resample
   results in modified values in the resampled images. New computations
   significantly reduce photometric errors. [#7894]
 
+- Improved compatibility with upcoming ``numpy 2.0`` that was affecting
+  decoding of context images and creation of masks. [#8059]
+
+source_catalog
+--------------
+
+- Made meta data flexible for photutils changes. [#8066]
+
+tweakreg
+--------
+
+- Improved how a image group name is determined. [#8012]
+
 
 1.12.5 (2023-10-19)
 ===================

README.md

@@ -9,7 +9,10 @@
 
 ![STScI Logo](docs/_static/stsci_logo.png)
 
-**JWST requires Python 3.9 or above and a C compiler for dependencies.**
+### JWST requires a C compiler for dependencies, and is currently limited to Python 3.9, 3.10 or 3.11.
+
+**Until Python 3.12 is supported, fresh conda environments will require setting the
+  python version to one of the three supported versions.**
 
 **Linux and MacOS platforms are tested and supported.  Windows is not currently supported.**
 
@@ -50,13 +53,13 @@ Remember that all conda operations must be done from within a bash/zsh shell.
 
 You can install the latest released version via `pip`.  From a bash/zsh shell:
 
-    conda create -n <env_name> python
+    conda create -n <env_name> python=3.11
     conda activate <env_name>
     pip install jwst
 
 You can also install a specific version:
 
-    conda create -n <env_name> python
+    conda create -n <env_name> python=3.11
     conda activate <env_name>
     pip install jwst==1.9.4
 
@@ -65,7 +68,7 @@ You can also install a specific version:
 You can install the latest development version (not as well tested) from the
 Github master branch:
 
-    conda create -n <env_name> python
+    conda create -n <env_name> python=3.11
     conda activate <env_name>
     pip install git+https://github.com/spacetelescope/jwst
 
@@ -117,7 +120,7 @@ already installed with released versions of the `jwst` package.
 
 As usual, the first two steps are to create and activate an environment:
 
-    conda create -n <env_name> python
+    conda create -n <env_name> python=3.11
     conda activate <env_name>
 
 To install your own copy of the code into that environment, you first need to

docs/index.rst

@@ -8,12 +8,6 @@
    :width: 400
    :align: center
 
-.. warning::
-
-   As of November 10, 2022, the process of deprecating the CRDS PUB Server will start.
-
-   For details, refer to the :ref:`pub-deprecation` page.
-
 Welcome to the documentation for `jwst`. This package contains the Python
 software suite for the James Webb Space Telescope (JWST) calibration pipeline,
 which processes data from all JWST instruments by applying various corrections to
@@ -46,14 +40,14 @@ desk at `JWST Help Desk <https://jwsthelp.stsci.edu>`_.
 
    jwst/user_documentation/introduction.rst
    jwst/user_documentation/reference_files_crds.rst
-   jwst/user_documentation/pub_deprecation.rst
    jwst/user_documentation/parameters.rst
    jwst/user_documentation/running_pipeline_python.rst
    jwst/user_documentation/running_pipeline_command_line.rst
    jwst/user_documentation/available_pipelines.rst
    jwst/user_documentation/input_output_file_conventions.rst
    jwst/user_documentation/logging_configuration.rst
    jwst/user_documentation/datamodels.rst
+   jwst/user_documentation/pub_deprecation.rst
 
 .. toctree::
    :maxdepth: 2

docs/jwst/user_documentation/reference_files_crds.rst

@@ -9,12 +9,6 @@ The JWST pipeline uses version-controlled :ref:`reference files <crds_reference_
 and set pipeline/step parameters, respectivley. These files both use the ASDF format,
 and are managed by the Calibration References Data System (:ref:`CRDS <crds>`) system.
 
-.. warning::
-
-   As of November 10, 2022, the process of deprecating the CRDS PUB Server will start.
-
-   For details, refer to the :ref:`pub-deprecation` page.
-
 .. _crds_reference_files:
 
 Reference Files

jwst/background/background_sub.py

@@ -3,6 +3,7 @@
 import numpy as np
 
 from stdatamodels.jwst import datamodels
+from stdatamodels.jwst.datamodels.dqflags import pixel
 
 from . import subtract_images
 from ..assign_wcs.util import create_grism_bbox
@@ -295,7 +296,12 @@ def subtract_wfss_bkg(input_model, bkg_filename, wl_range_name, mmag_extract=Non
     # i.e. in regions we can use as background.
     if got_catalog:
         bkg_mask = mask_from_source_cat(input_model, wl_range_name, mmag_extract)
-        if bkg_mask.sum() < 100:
+        # Ensure mask has 100 pixels and that those pixels correspond to valid
+        # pixels using model DQ array
+        if np.count_nonzero(input_model.dq[bkg_mask]
+                            ^ pixel['DO_NOT_USE']
+                            & pixel['DO_NOT_USE']
+                            ) < 100:
             log.warning("Not enough background pixels to work with.")
             log.warning("Step will be SKIPPED.")
             return None

jwst/extract_1d/soss_extract/atoca_utils.py

@@ -228,7 +228,7 @@ def get_wv_map_bounds(wave_map, dispersion_axis=1):
 
         # Compute the change in wavelength for valid cols
         idx_valid = np.isfinite(wave_col)
-        idx_valid &= (wave_col > 0)
+        idx_valid &= (wave_col >= 0)
         wv_col_valid = wave_col[idx_valid]
         delta_wave = np.diff(wv_col_valid)