.gitignore

+!.gitignore
+!.gitlab-ci.yml
+.*
+desktop.ini
+*.pyc
+*.egg-info
+*.DS_Store
+*.DS
+*.ipynb_checkpoints*
+build/*
+docs/_build/*
+dist/*
+src/empyre/version.py
+htmlcov/
+coverage.xml

.gitlab-ci.yml

+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+    - if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS
+      when: never
+    - if: $CI_COMMIT_BRANCH
+    - if: $CI_COMMIT_TAG
+
+before_script:
+    # Install requirements for empyre:
+    - source ${CONDA_DIR}/etc/profile.d/conda.sh
+    - conda create -q --name empyre # -q: quiet/ no progressbar, because it spams the log!
+    - conda activate empyre
+    - conda install -y python numpy sphinx pip setuptools jupyter pandoc uv
+    - uv pip install .[tests,docs]
+    - conda info --envs
+    # Install jutil via deploy token access:  # TODO: still needed?
+    #- pip install git+https://empyre:"$JUTIL_DEPLOY_TOKEN"@jugit.fz-juelich.de/j.ungermann/jutil.git
+
+stages:
+    - test
+    - deploy
+
+test_style:
+    stage: test
+    image: condaforge/miniforge3:latest
+    script:
+        - pip install pre-commit
+        - pre-commit install
+        - pre-commit run --all-files
+
+test_function:
+    stage: test
+    image: condaforge/miniforge3:latest
+    script:
+        # Execute all tests and also check coverage with --cov:
+        - pip install "numpy>=2"
+        - pytest --cov
+    artifacts:
+        paths:
+            - .coverage
+        expire_in: 1 week
+
+test_docs:
+    stage: test
+    image: condaforge/miniforge3:latest
+    script:
+        # -f: Force overwriting of any existing generated files.
+        # -e: Put documentation for each module on its own page.
+        # -o: Directory to place the output files. If it does not exist, it is created.
+        # last parameter: module path
+        # - python setup.py  clean  # TODO: Simplest way to generate version.py without doing anything else?
+        #- sphinx-apidoc -f -e -o docs/api src/empyre
+        # Build the documentation from 'docs' and put into 'build/sphinx':
+        - sphinx-build docs build/sphinx -W  # -w fails the build if warnings appear!
+    artifacts:
+        paths:
+            - build/sphinx
+        expire_in: 1 week
+
+test_install:
+    stage: test
+    image: condaforge/miniforge3:latest
+    before_script: []  # before_script not needed here!
+    script:
+        - conda install -y "python<3.12"
+        - pip install .[all]
+
+pages:
+    stage: deploy
+    image: busybox
+    before_script: []  # before_script not needed here!
+    script:
+        - mkdir public
+        - cp -r build/sphinx/* public/
+        # -r: recursive, also copies subfolders!
+    artifacts:
+        paths:
+            - public
+    rules:
+        - if:  '$CI_COMMIT_BRANCH == "master" || $CI_COMMIT_TAG =~ /^\d+\.\d+(\.\d+)?$/'
+
+pypi:
+    stage: deploy
+    image: condaforge/miniforge3:latest
+    before_script: []  # before_script not needed here!
+    script:
+        - pip install hatch twine
+        - hatch build
+        - twine upload -u __token__ -p $PYPI_ACCESS_TOKEN dist/*  # -u user -p password upload_source
+    rules:  # similar to only/except, but newer!
+        # Job is executed if branch is master AND if a tag is building which matches the regular expression!
+        # ONLY executes if commit to master has a tag, ^:start, $:end, valid example: "1.2.3", no "-dev" at the end!
+        - if: '$CI_COMMIT_TAG =~ /^\d+\.\d+(\.\d+)?$/'

.gitlab/issue_templates/bug.md

+<!--
+Please read this!
+
+Before opening a new issue, make sure to search for keywords in the issues
+filtered by the "bug" label:
+- https://iffgit.fz-juelich.de/empyre/empyre/issues?label_name%5B%5D=bug
+
+and verify the issue you're about to submit isn't a duplicate.
+-->
+
+### Summary
+
+<!-- Summarize the bug encountered concisely. -->
+
+### Steps to reproduce
+
+<!-- How one can reproduce the issue - this is very important. -->
+
+### What is the current *bug* behavior?
+
+<!-- What actually happens. -->
+
+### What is the expected *correct* behavior?
+
+<!-- What you should see instead. -->
+
+### Relevant logs and/or screenshots
+
+<!-- Paste any relevant logs - please use code blocks (```) to format console output,
+logs, and code as it's tough to read otherwise.. -->
+
+### Possible fixes
+
+<!-- If you can, link to the line of code that might be responsible for the problem. -->
+
+~bug

.gitlab/issue_templates/feature request.md

+### Problem to solve
+
+<!-- What problem do we solve? -->
+
+### Intended users
+
+<!-- Who will use this feature? . It's okay to write "Unknown" and fill this field in later. -->
+
+### Further details
+
+<!-- Include use cases, benefits, and/or goals -->
+
+### Proposal
+
+<!-- How are we going to solve the problem? -->
+
+### Documentation
+
+<!-- Add all known Documentation Requirements here. -->
+
+~feature
\ No newline at end of file

.pre-commit-config.yaml

+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: trailing-whitespace
+    files: ^src/
+  - id: end-of-file-fixer
+    files: ^src/
+  - id: check-yaml
+  - id: check-added-large-files
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+    exclude: ^prototypes/
+- repo: https://github.com/regebro/pyroma
+  rev: "4.2"
+  hooks:
+  - id: pyroma
\ No newline at end of file

Igor/Igor Shared Procedures/Append Residuals.ipf

-#pragma rtGlobals=3		// Use modern global access method and strict wave access.
-
-Menu "Macros"
-	"Append Residuals...", AppendResidualsDialog()
-End
-
-Function AppendResiduals(ywave,xwave)
-	String ywave, xwave
-	if  (CmpStr("_calculated_",xwave) == 0)
-		AppendToGraph/L=Lresid $ywave
-	else 
-		AppendToGraph/L=Lresid $ywave vs $xwave
-	endif
-	ModifyGraph nticks(Lresid)=2,standoff(bottom)=0, axisEnab(left)={0,0.7}
-	ModifyGraph axisEnab(Lresid)={0.8,1}, freePos(Lresid)=0
-	SetAxis/A/E=2 Lresid
-	ModifyGraph mode(histResids)=2, lsize(histResids)=2
-End
-
-Function AppendResidualsDialog()
-	String ywave, xwave
-	Prompt ywave, "Residuals Data", popup WaveList("*",";","")
-	Prompt xwave, "X Data", popup "_calculated_;"+WaveList("*",";","")
-	DoPrompt "Append Residuals", ywave, xwave
-	if (V_flag != 0)
-		return -1;		//User canceled.
-	endif
-	AppendResiduals(ywave,xwave)
-End
\ No newline at end of file

Igor/desktop.ini

-[.ShellClassInfo]
-IconResource=C:\Windows\system32\SHELL32.dll,4
-[ViewState]
-Mode=
-Vid=
-FolderType=Generic