Merge branch 'develop' into specify-pids-for-preview-image-creation

.github/workflows/build.yml

@@ -14,7 +14,9 @@ jobs:
   build:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
     with:
-      upload_to_pypi: false
+      upload_to_pypi: ${{ (github.event_name == 'release') && (github.event.action == 'released') }}
+    secrets:
+      pypi_token: ${{ secrets.PYPI_PASSWORD_STSCI_MAINTAINER }}
   freeze:
     runs-on: ${{ matrix.os }}
     strategy:

.gitignore

@@ -19,3 +19,4 @@ jwql/website/apps/jwql/static/filesystem
 jwql/website/apps/jwql/static/outputs
 jwql/website/apps/jwql/static/preview_images
 jwql/website/apps/jwql/static/thumbnails
+jwql-current.yml

CHANGES.rst

@@ -1,5 +1,46 @@
 ## What's Changed
 
+1.2.10 (2024-07-10)
+===================
+
+Duplicate of 1.2.9, caused by changes to versioning conflicts with pypi. 
+
+
+1.2.9 (2024-07-10)
+==================
+
+Web Application
+~~~~~~~~~~~~~~~
+- Add Download CSV button to query page by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1561
+- show file anomalies on exposure group page by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1564
+- create generic error page to handle exceptions in views. by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1549
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+- final model define for faking by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1544
+- Update Redis Package Names in Environment Files by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1546
+- [SCSB-145] require Python 3.10 by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1515
+- debug false by default by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1550
+- Update NIRSpec TA Monitors to use Django DB Models by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1499
+- Update NIRSpec TA Models by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1565
+- Remove codecov.yml by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1588
+- Remove filename parser test over filesystem by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1586
+- Update remote to upstream in pull_jwql_branch.sh by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1591
+- Add Dependencies for Servers in `pyproject.toml` by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1568
+- fix release upload step condition to match workflow trigger by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1593
+- fix environment freeze workflow not picking up tag by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1594
+- fix version matching pattern by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1595
+- updating freeze matrix to include linux, mac and python 3.12 by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1596
+- Remove P750L from list of NIRSpec filters by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1598
+- [build] fix `runs-on:` and update build filename for easier parsing by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1599
+- upload to PyPI on release by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1601
+- Updating jwst_reffiles version number by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1606
+- Remove old presentations from repo by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1607
+- Num results fix by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1608
+- Add Environment Update Script by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1609
+- Add new NIRISS AMI-related suffixes by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1613
+
+
 1.2.8 (2024-04-18)
 ==================
 

jwql/install-env.sh

@@ -0,0 +1,70 @@
+branchname=$1
+python_version=$2
+
+printf "UPDATING JWQL ENVIRONMENT\n\n"
+
+# Check operating system to obtain proper substring for environment
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    os_str="macOS_ARM64"
+    printf "INFORMATION: \n \t MAC OS DETECTED, USING MAC ENVIRONMENT FILE\n"
+elif [[ "$OSTYPE" == "linux-gnu"* ]]; then
+    os_str="Linux_X64"
+    printf "INFORMATION: \n \t LINUX OS DETECTED, USING LINUX ENVIRONMENT FILE\n"
+else
+    printf "EXCEPTION: \n \t $OSTYPE NOT SUPPORTED, EXITING"
+    return
+fi
+
+# Check if branch name starts with "v" for our major releases
+# Our branch names contain v prior to version number, but version names on git
+# do not contain v prior to the number.
+if [[ $branchname == v* ]]; then
+    jwql_version=${branchname:1:${#branchname}}
+    environment_url=https://github.com/spacetelescope/jwql/releases/download/$jwql_version/
+    environment_name=jwql_${jwql_version}_conda_${os_str}_py${python_version}
+    environment_filename="${environment_name}.yml"
+else
+    printf "EXCEPTION: \n \t RELEASE DOESNT FOLLOW RELEASE VERSIONING NAMING CONVENTION, EXITING"
+    return
+fi
+
+# Download asset from release and install it.
+if curl --head --silent --fail "${environment_url}${environment_filename}" 2> /dev/null;
+    then
+        # Reset back to base first before generating environment (incase one is currently activated)
+        eval "$(conda shell.bash deactivate)"
+        eval "$(conda shell.bash activate base)"
+        printf "\n SUCESSFULLY LOCATED ENVIRONMENT FILE ${environment_url}${environment_filename} \n"
+        curl -L "${environment_url}/${environment_filename}" > jwql-current.yml
+        $CONDA_EXE env create --name $environment_name --file jwql-current.yml
+    else
+        printf "EXCEPTION:\n"
+        printf "\t ${environment_url}${environment_filename} DOES NOT EXIST, EXITING\n"
+        printf "\t \nENSURE THAT: \n"
+        printf "\t https://github.com/spacetelescope/jwql/releases/tag/$branchname \n"
+        printf "EXISTS AND VERIFY ASSET FOR ${jwql_version}, ${python_version} FOR OS ${os_str}"
+        return
+fi
+
+# Update symlink
+cd ${CONDA_PREFIX}/envs/
+
+env_symlink="jwql-current"
+
+if [[ -L $env_symlink || -e $env_symlink ]]; then
+   printf "INFORMATION:\n"
+   printf "\tjwql-current SYMLINK EXISTS, UNLINKING\n"
+   unlink jwql-current
+fi
+
+printf "INFORMATION:\n\tLINKING NEW ENVIRONMENT\n"
+ln -s $environment_name jwql-current
+
+printf "\tjwql-current HAS BEEN SET TO: ${environment_name}\n"
+printf "\tTO SEE CHANGES, EXIT/RESTART SHELL\n"
+
+# return to original directory
+cd -
+
+# Conda commands change shell prompt, this just returns it to the default
+export PS1="\n(base)\h:\W \u\$ "

jwql/utils/constants.py

@@ -785,7 +785,7 @@
 ]
 
 # Possible suffix types for AMI files
-NIRISS_AMI_SUFFIX_TYPES = ["amiavg", "aminorm", "ami", "psf-amiavg"]
+NIRISS_AMI_SUFFIX_TYPES = ["amiavg", "aminorm", "ami", "psf-amiavg", "psf-ami-oi", "ami-oi", "aminorm-oi", "amimulti-oi", "amilg"]
 
 # Determine if the code is being run as part of CI checking on github
 ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')

jwql/utils/preview_image.py

@@ -490,16 +490,54 @@ def make_figure(self, image, integration_number, min_value, max_value,
                     dig = 2
                 format_string = "%.{}f".format(dig)
                 tlabelstr = [format_string % number for number in tlabelflt]
-                cbar = self.fig.colorbar(cax, ticks=tickvals)
 
                 # This seems to correctly remove the ticks and labels we want to remove. It gives a warning that
                 # it doesn't work on log scales, which we don't care about. So let's ignore that warning.
                 warnings.filterwarnings("ignore", message="AutoMinorLocator does not work with logarithmic scale")
-                cbar.ax.yaxis.set_minor_locator(AutoMinorLocator(n=0))
 
-                cbar.ax.set_yticklabels(tlabelstr)
-                cbar.ax.tick_params(labelsize=maxsize * 5. / 4)
-                cbar.ax.set_ylabel(self.units, labelpad=10, rotation=270)
+                xyratio = xsize / ysize
+                if xyratio < 1.6:
+                    # For apertures that are taller than they are wide, square, or that are wider than
+                    # they are tall but still reasonably close to square, put the colorbar on the right
+                    # side of the image.
+
+                    # Some magic numbers arrived at through testing aspect ratios for all apertures
+                    if xyratio > 0.4:
+                        cb_width = 0.05
+                    else:
+                        cb_width = 0.05 * 0.4 / xyratio
+
+                    upper_x_anchor = 0.02
+                    if xyratio < 0.1:
+                        upper_x_anchor = 0.12
+
+                    cbax = self.fig.add_axes([ax.get_position().x1 + upper_x_anchor,
+                                              ax.get_position().y0,
+                                              cb_width,
+                                              ax.get_position().height
+                                              ])
+                    cbar = self.fig.colorbar(cax, cax=cbax, ticks=tickvals, orientation='vertical')
+                    cbar.ax.yaxis.set_minor_locator(AutoMinorLocator(n=0))
+                    cbar.ax.set_yticklabels(tlabelstr)
+                    cbar.ax.set_ylabel(self.units, labelpad=7, rotation=270)
+                else:
+                    # For apertures that are significantly wider than they are tall, put the colorbar
+                    # under the image.
+
+                    # Again, some magic numbers controlling the positioning and height of the
+                    # colorbar, based on testing.
+                    lower_y_anchor = 0. - (xyratio / 14.5)
+                    cb_height = 0.07 * (np.log2(xyratio) - 1)
+
+                    cbax = self.fig.add_axes([ax.get_position().x0,
+                                              ax.get_position().y0 + lower_y_anchor,
+                                              ax.get_position().width,
+                                              cb_height])
+                    cbar = self.fig.colorbar(cax, cax=cbax, ticks=tickvals, orientation='horizontal')
+                    cbar.ax.xaxis.set_minor_locator(AutoMinorLocator(n=0))
+                    cbar.ax.set_xticklabels(tlabelstr)
+                    cbar.ax.set_xlabel(self.units, labelpad=7, rotation=0)
+
                 ax.set_xlabel('Pixels', fontsize=maxsize * 5. / 4)
                 ax.set_ylabel('Pixels', fontsize=maxsize * 5. / 4)
                 ax.tick_params(labelsize=maxsize)

jwql/utils/utils.py

@@ -530,7 +530,8 @@ def filename_parser(filename):
         time_series,
         time_series_2c,
         guider,
-        guider_segment]
+        guider_segment
+    ]
 
     filename_type_names = [
         'stage_1_and_2',

jwql/website/apps/jwql/forms.py

@@ -160,7 +160,7 @@ class JwqlQueryForm(BaseForm):
     num_choices = [(50, 50), (100, 100), (200, 200), (500, 500)]
     num_per_page = forms.ChoiceField(
         required=True,
-        choices=num_choices, initial=num_choices[1],
+        choices=num_choices, initial=num_choices[3],
         widget=forms.RadioSelect)
 
     # instrument specific parameters

jwql/website/apps/jwql/views.py

@@ -131,6 +131,7 @@ def jwql_query(request):
             parameters[QueryConfigKeys.DATE_RANGE] = form.cleaned_data['date_range']
             parameters[QueryConfigKeys.PROPOSAL_CATEGORY] = form.cleaned_data['proposal_category']
             parameters[QueryConfigKeys.SORT_TYPE] = form.cleaned_data['sort_type']
+            parameters[QueryConfigKeys.NUM_PER_PAGE] = form.cleaned_data['num_per_page']
             parameters[QueryConfigKeys.ANOMALIES] = all_anomalies
             parameters[QueryConfigKeys.APERTURES] = all_apers
             parameters[QueryConfigKeys.FILTERS] = all_filters

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     "jsonschema>=4.21.1,<5",
     "jwst>=1.13.4,<2",
     "jwst_backgrounds>=1.2.0,<1.3.0",
-    "jwst_reffiles@git+https://github.com/spacetelescope/jwst_reffiles",
+    "jwst_reffiles>=1.0.1",
     "matplotlib>=3.8.3,<4",
     "numpy>=1.26.4,<2",
     "pandas>=2.2.1,<3",

style_guide/example.py

@@ -73,7 +73,7 @@
 
 # Global variables should be avoided, but if used should be named with
 # all-caps
-A_GLOBAL_VARIABLE = 'foo'  # type: str
+A_GLOBAL_VARIABLE = "foo"  # type: str
 
 
 @log_fail
@@ -92,14 +92,14 @@ def my_main_function(path: str, filter: str) -> None:
         The filter to process (e.g. "F606W").
     """
 
-    logging.info('Using {} as an input file'.format(path))
+    logging.info("Using {} as an input file".format(path))
 
     an_int = 1  # type: int
     a_float = 3.14  # type: float
     a_bool = True  # type: bool
-    a_list = ['Dog', 'Cat', 'Turtle', False, 7]  # type: List[Union[str, bool, int]]
-    a_tuple = ('Dog', 'Cat', 'Turtle', False, 7)  # type: Tuple[str, str, str, bool, int]
-    a_dict = {'key1': 'value1', 'key2': 'value2'}  # type: Dict[str, str]
+    a_list = ["Dog", "Cat", "Turtle", False, 7]  # type: List[Union[str, bool, int]]
+    a_tuple = ("Dog", "Cat", "Turtle", False, 7)  # type: Tuple[str, str, str, bool, int]
+    a_dict = {"key1": "value1", "key2": "value2"}  # type: Dict[str, str]
     an_obj = object()  # type: object
 
     result = some_other_function(an_int, a_float, a_bool, a_list, a_tuple, a_dict, an_obj)  # type: Optional[int]
@@ -117,21 +117,13 @@ def parse_args() -> argparse.Namespace:
     """
 
     # Create help strings
-    path_help = 'The path to the input file.'  # type: str
+    path_help = "The path to the input file."  # type: str
     filter_help = 'The filter to process (e.g. "F606W").'  # type: str
 
     # Add arguments
     parser = argparse.ArgumentParser()  # type: argparse.ArgumentParser
-    parser.add_argument('path',
-                        type=str,
-                        default=os.getcwd(),
-                        help=path_help)
-    parser.add_argument('-f --filter',
-                        dest='filter',
-                        type=str,
-                        required=False,
-                        default='F606W',
-                        help=filter_help)
+    parser.add_argument("path", type=str, default=os.getcwd(), help=path_help)
+    parser.add_argument("-f --filter", dest="filter", type=str, required=False, default="F606W", help=filter_help)
 
     # Parse args
     args = parser.parse_args()  # type: argparse.Namespace
@@ -140,8 +132,7 @@ def parse_args() -> argparse.Namespace:
 
 
 @log_timing
-def some_other_function(an_int: int, a_float: float, a_bool: bool, a_list: List[Any],
-                        a_tuple: Tuple[Any], a_dict: Dict[Any, Any], an_obj: object) -> int:
+def some_other_function(an_int: int, a_float: float, a_bool: bool, a_list: List[Any], a_tuple: Tuple[Any], a_dict: Dict[Any, Any], an_obj: object) -> int:
     """This function just does a bunch of nonsense.
 
     But it serves as a decent example of some things.
@@ -170,19 +161,18 @@ def some_other_function(an_int: int, a_float: float, a_bool: bool, a_list: List[
     """
 
     # File I/O should be handeled with 'with open' when possible
-    with open('my_file', 'w') as f:
-        f.write('My favorite integer is {}'.format(an_int))
+    with open("my_file", "w") as f:
+        f.write("My favorite integer is {}".format(an_int))
 
     # Operators should be separated by spaces
     logging.info(a_float + a_float)
 
     return an_int
 
 
-if __name__ == '__main__':
-
+if __name__ == "__main__":
     # Configure logging
-    module = os.path.basename(__file__).strip('.py')
+    module = os.path.basename(__file__).strip(".py")
     configure_logging(module)
 
     args = parse_args()  # type: argparse.Namespace

style_guide/typing_demo/typing_demo_1.py

@@ -7,8 +7,7 @@
 """
 
 import sys
-from typing import (List, Set, Dict, Tuple, Union, Optional, Callable,
-                    Iterable, Any)
+from typing import Any, Callable, Dict, Iterable, List, Optional, Set, Tuple, Union
 
 assert sys.version_info >= (3, 6)  # PEP 526 added variable annotations
 
@@ -18,7 +17,7 @@
 a_string: str = "jwql"
 a_list: List[int] = [1]
 a_set: Set[int] = {1, 2, 3}
-a_dict: Dict[str, bool] = {'jwql': True}  # Have to specify both keys and values
+a_dict: Dict[str, bool] = {"jwql": True}  # Have to specify both keys and values
 
 # For python versions prior to 3.6, the variable annotation syntax uses comments:
 #    annotated_variable = 1 # type: int
@@ -68,6 +67,7 @@ def a_generator() -> Iterable[int]:
 # Type annotations are stored in __annotations__, either as a local variable
 # or as an object attribute.
 
+
 def print_annotations(arg: Any) -> bool:
     if not hasattr(arg, "__annotations__"):
         print("Sorry, that argument doesn't have its own __annotations__.")
@@ -76,8 +76,7 @@ def print_annotations(arg: Any) -> bool:
     return bool(arg.__annotations__)
 
 
-for name in ["an_integer", "a_generic_function", "two_arg_function",
-             "func_alias", "anon_func", "a_generator"]:
+for name in ["an_integer", "a_generic_function", "two_arg_function", "func_alias", "anon_func", "a_generator"]:
     var = locals()[name]
     print(f"Annotations for {name}:")
     if not print_annotations(var):