Merge branch 'develop' into miri_improvements

.github/ISSUE_TEMPLATE/bug-template.yml

@@ -0,0 +1,72 @@
+name: Bug Report
+description: File a bug report
+title: "[Bug]: "
+labels: ["bug"]
+body:
+  - type: checkboxes
+    id: verify
+    attributes:
+      label: Check Existing Issues
+      description: |
+        Before submitting this issue, please confirm the following:
+      options:
+        - label: Yes, I have checked existing issues to ensure this problem hasn't already been reported.
+          required: true
+  - type: dropdown
+    id: instrument
+    attributes:
+      label: Instrument or Category
+      description: Which instrument or piece of code were you running?
+      multiple: true
+      options:
+        - NIRCam Stage 1/2 Pipeline
+        - MIRI Stage 1/2 Pipeline
+        - Image Tools
+        - PSF Subtraction
+        - Analysis Tools
+        - Other
+    validations:
+      required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Please describe what happened and/or what you expected to happen.
+      placeholder: Describe the issue and/or expected outcome.
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Error traceback output
+      description: Please copy and paste the full traceback of the error you encountered.
+      placeholder: Paste the error traceback here.
+    validations:
+      required: false
+  - type: input
+    id: OS
+    attributes:
+      label: What operating system are you using?
+      placeholder: E.g., Windows 11; Mac OS 10.10 El Capitan
+  - type: input
+    id: python_version
+    attributes:
+      label: What version of Python are you running?
+      description: If you're not sure, open a terminal with the environment you're running spaceKLIP in and type "python --version"
+      placeholder: E.g., Python 3.7
+  - type: textarea
+    id: package_list
+    attributes:
+      label: What Python packages do you have installed?
+      description: To get a full list, open a terminal with the environment you're running spaceKLIP in and type "conda list". Paste the full output here.
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional context or information
+      description: |
+        Provide any additional context or information that might be relevant to this issue.
+      placeholder: Add any additional context or information here.
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report! After you submit this issue, check this GitHub thread for any updates/responses from the spaceKLIP team.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/documentation-template.yml

@@ -0,0 +1,43 @@
+name: Documentation Issue or Request
+description: Report issues or suggest improvements to the spaceKLIP documentation.
+title: "[Documentation]: "
+labels: ["documentation"]
+body:
+  - type: checkboxes
+    id: verify
+    attributes:
+      label: Check Existing Issues
+      description: |
+        Before submitting this issue, please confirm the following:
+      options:
+        - label: Yes, I have checked existing issues to ensure this problem hasn't already been reported.
+          required: true
+  - type: textarea
+    id: problem-description
+    attributes:
+      label: Describe the issue or suggest an improvement
+      description: |
+        Please describe any issues with our documentation or suggest improvements. Your feedback is appreciated!
+      placeholder: Describe the issue or suggest improvements here.
+    validations:
+      required: true
+  - type: textarea
+    id: page-urls
+    attributes:
+      label: URLs of the documentation pages (if applicable)
+      description: |
+        If the issue is specific to particular pages, provide the URLs here.
+        This helps us locate and address the issue more efficiently. You can list multiple URLs if needed.
+      placeholder: Enter the URLs.
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional context or information
+      description: |
+        Provide any additional context or information that might be relevant to this issue or suggestion.
+      placeholder: Add any additional context or information here.
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for helping us improve our documentation! After you submit this issue, check this GitHub thread for any updates/responses from the spaceKLIP team.
+

.github/ISSUE_TEMPLATE/improvement-template.yml

@@ -0,0 +1,53 @@
+name: Enhancement Suggestion
+description: Suggest an enhancement to spaceKLIP
+title: "[Enhancement]: "
+labels: ["enhancement"]
+body:
+  - type: dropdown
+    id: instrument
+    attributes:
+      label: Instrument or Category
+      description: Which instrument or piece of code would you like to see improved?
+      multiple: true
+      options:
+        - NIRCam Stage 1/2 Pipeline
+        - MIRI Stage 1/2 Pipeline
+        - Image Tools
+        - PSF Subtraction
+        - Analysis Tools
+        - Other
+    validations:
+      required: true
+  - type: textarea
+    id: suggestion
+    attributes:
+      label: What is your suggestion?
+      description: What feature would you like to see in spaceKLIP?
+      placeholder: It would be super helpful if spaceKLIP did...
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Error traceback output
+      description: If relevant, please copy and paste the full traceback of any errors you encountered.
+  - type: input
+    id: OS
+    attributes:
+      label: What operating system are you using?
+      placeholder: E.g., Windows 11; Mac OS 10.10 El Capitan
+  - type: input
+    id: python_version
+    attributes:
+      label: What version of Python are you running?
+      description: If you're not sure, open a terminal with the environment you're running spaceKLIP in and type "python --version"
+      placeholder: E.g., Python 3.7
+  - type: textarea
+    id: package_list
+    attributes:
+      label: What Python packages do you have installed?
+      description: To get a full list, open a terminal with the environment you're running spaceKLIP in and type "conda list". Paste the full output here.
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to suggest an enhancement! After you submit this issue, check this GitHub thread for any updates/responses from the spaceKLIP team.

.github/workflows/autolabel.yml

@@ -0,0 +1,14 @@
+name: "Set Issue Label and Assignee"
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: Naturalclar/[email protected]
+        with:
+          title-or-body: "both"
+          parameters: '[ {"keywords": ["NIRCam Stage 1/2 Pipeline"], "labels": ["NIRCam"], "assignees": ["AarynnCarter","mperrin","JarronL"]}, {"keywords": ["MIRI Stage 1/2 Pipeline"], "labels": ["MIRI"], "assignees": ["AarynnCarter","mperrin","JarronL"]}, {"keywords": ["Image Tools"], "labels": ["image tools"], "assignees": ["kglidic","kammerje","AarynnCarter","wbalmer","kdlawson","JarronL"]}, {"keywords": ["PSF Subtraction"], "labels": ["PSF subtraction"], "assignees": ["kdlawson","wbalmer","AarynnCarter"]}, {"keywords": ["Analysis Tools"], "labels": ["analysis tools"], "assignees": ["kdlawson","wbalmer","AarynnCarter","juliengirard","kammerje","kglidic"]}, {"keywords": ["Other"], "labels": ["other"], "assignees": ["kdlawson","AarynnCarter","juliengirard","JarronL","kglidic"]}, {"keywords": ["Documentation"], "labels": ["documentation"], "assignees": ["AarynnCarter","mperrin","kglidic"]}]'
+          github-token: "${{ secrets.GITHUB_TOKEN }}"

README.rst

@@ -37,15 +37,11 @@ With the Anaconda environment created, move to the cloned directory and install
 ::
 
 	cd where/you/saved/the/git/repo
+	conda install conda-forge::git-lfs	
 	pip install -r requirements.txt
 	pip install -e .
 
-NEW AS OF 1 JUNE 2023: you also need to make the custom PSF mask files before running spaceKLIP for the first time:
-
-::
-
-	cd spaceKLIP/
-        python make_psfmasks.py
+Note that installing git-lfs from pip does not work as of 25 June 2024.
 
 Finally, and very importantly, you will need to download the reference files and set the environment variables supporting the functioning of :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF <https://webbpsf.readthedocs.io/en/latest/installation.html#installing-the-required-data-files>`_, `WebbPSF_ext <https://github.com/JarronL/webbpsf_ext>`_). Ensure that if you edit your .bashrc file, close and reopen your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work).
 

requirements.txt

@@ -9,4 +9,4 @@ scipy
 stsci.stimage==0.2.6
 webbpsf
 webbpsf_ext>=1.2.0
-pyklip @ git+https://bitbucket.org/pyKLIP/pyklip.git@jwst
+pyklip