Merge branch 'devel' into fix/119-listdir-matching-tests

Author: ehrenfeu

.github/workflows/lint.yml

@@ -1,23 +1,36 @@
-name: Code Linting 🔎⚡
+name: Linting 📑🔎⚡
 
 on:
   push:
   pull_request:
   workflow_dispatch:
 
 jobs:
-
-  lint:
+  ruff:
     name: Ruff ⚡🕵
 
     runs-on: ubuntu-latest
 
     steps:
-
       - name: 📥 Checkout repo
         uses: actions/checkout@v4
 
       - name: Run Ruff checks ⚡
         uses: astral-sh/ruff-action@v3
         with:
           args: check
+
+  markdownlint:
+    name: Markdownlint 📑🕵
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: 📥 Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Run markdownlint-cli2-action 📑
+        uses: DavidAnson/markdownlint-cli2-action@v22
+        with:
+          globs: |
+            *.md
+            !test/*.md

.vscode/settings.json

@@ -15,31 +15,56 @@
         "bdvp",
         "bigstitcher",
         "biop",
+        "clij",
+        "Dscijava",
+        "flatfield",
+        "Fluo",
+        "IJPB",
         "imageplus",
+        "imarisconvert",
         "imglib",
+        "imgplus",
         "interestpoint",
         "intermodes",
         "javax",
+        "keyvalue",
         "Kheops",
+        "labelimage",
+        "listdir",
         "micrometa",
+        "Morpholib",
         "multiresolution",
+        "olefile",
+        "omerotools",
+        "ordereddict",
         "otsu",
         "pathtools",
+        "phmax",
         "Prefs",
+        "processingoptions",
         "PTBIOP",
         "PYENV",
         "pylint",
         "ransac",
         "renyi",
         "repartitions",
+        "resultstable",
         "RETVAL",
+        "roimanager",
+        "rois",
+        "rollingball",
         "scijava",
         "shanbhag",
         "sjlogging",
+        "smtpserver",
         "spimdata",
+        "stardist",
+        "stdv",
         "strtools",
         "subfolders",
         "subsampling",
+        "TESTDATA",
+        "thresholding",
         "trackmate",
         "virtualenv",
         "virtualfish"

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 # Changelog 🧾
 
+## 2.0.0
+
+### Changed
+
+* Minimum required version for [python-micrometa] increased to `15.2.3`.
+
 ## 1.5.0
 
 This release brings a lot of additions, not all changes and functions are
@@ -271,3 +277,5 @@ Utilities for filtering and thresholding.
 * `imcflibs.pathtools.listdir_matching` now has an additional optional argument
   `sort` (defaulting to `False`) to request the resulting list to be sorted.
 * Many improvements / clarifications in function docstrings.
+
+[python-micrometa]: https://pypi.org/project/python-micrometa/

DESC.md

@@ -1,2 +1,4 @@
+<!-- markdownlint-disable MD041 (first-line-heading) -->
+
 :snake::coffee::nut_and_bolt::wrench:
 A collection of commonly used Python helper functions.

DEVELOPMENT.md

@@ -30,7 +30,7 @@ RELEASE_TAG=$(git tag -l "python-imcflibs-*" | tail -n 1)
 git push origin $RELEASE_TAG
 ```
 
-**IMPORTANT 2**: in case a **pre-releaes** was created, the last commit needs to
+**IMPORTANT 2**: in case a **pre-release** was created, the last commit needs to
 be discarded as the *release-script* places a wrong version / snapshot
 combination in the `pom.xml`:
 

README.md

@@ -10,28 +10,81 @@
 [![DOI](https://zenodo.org/badge/156891364.svg)][doi]
 
 This package contains a diverse collection of Python functions dealing with
-paths, I/O (file handles, ...), strings etc. and tons of [Fiji][fiji] /
-[ImageJ2][imagej] convenience wrappers to simplify scripting and reduce
-cross-script redundanciees.
+paths, I/O (file handles, ...), strings etc. and tons of [Fiji] / [ImageJ2]
+convenience wrappers to simplify scripting and reduce cross-script redundancies.
 
 Initially this has been a multi-purpose package where a substantial part had
-been useful in **CPython** as well. However, since the latest Jython
-release is still based on Python 2.7 (see the [Jython 3 roadmap][jython3] for
-more info), *imcflibs* is now basically limited to the **Fiji / ImageJ2
-ecosystem**.
+been useful in **CPython** as well. However, since the latest Jython release is
+still based on Python 2.7 (see the [Jython 3 roadmap][jython3] for more info),
+*imcflibs* is now basically limited to the **Fiji / ImageJ2 ecosystem**.
 
 Releases are made through Maven and published to the [SciJava Maven
 repository][sj_maven]. The easiest way to use the lib is by adding the **`IMCF
 Uni Basel`** [update site][imcf_updsite] to your ImageJ installation.
 
 The [`pip install`able package][pypi] is probably only useful for two cases:
 running `pytest` (where applicable) and rendering [HTML-based API docs][apidocs]
-using [`pdoc`][pdoc]. Let us know in case you're having another use case 🎪 for
-it.
+using [pdoc]. Let us know in case you're having another use case 🎪 for it.
 
 Developed and provided by the [Imaging Core Facility (IMCF)][imcf] of the
 Biozentrum, University of Basel, Switzerland.
 
+## Installation Instructions
+
+Two ways of installing the `imcflibs` package are described here, the "*easy*"
+one through the *Fiji Update Sites* and the "*manual*" method using packages
+explicitly downloaded from [SciJava Maven][sj_maven].
+
+### 🧿 Default: Installation via Update Sites
+
+After a fresh install of [Fiji], navigate to *Help* -> *Update* and in the
+resulting window, press *Manage Update Sites*. Here, search for and tick the
+following necessary update sites for this package.
+
+- ImageJ
+- Fiji
+- 3D ImageJ-Suite
+- clij2
+- IJPB-plugins
+- IMCF Uni Basel
+- StarDist
+- CALM
+- TrackMate-Cellpose
+- TrackMate-Helper
+- TrackMate-StarDist
+- TrackMate-Weka
+- TrackMate-MorpholibJ
+
+The **`IMCF Uni Basel`** update-site will always provide the latest compatible
+combination of *official*`.jar` file to use this package.
+
+### 🏗 Alternative: SciJava Maven Package 👷
+
+💡 **IMPORTANT:** 💡 same as for the *default* installation previously
+described, you will need to enable **all Update Sites listed above** in your
+Fiji as well when using the method described here!
+
+The most up-to-date `.jar` (or any other published version, including
+pre-releases) for this package can be always found on the [Scijava Maven
+repository][sj_maven]. Navigate to the `python-imcflibs` folder, pick the
+desired version (can also be a pre-release) and download the contained `.jar`
+file, e.g. `python-imcflibs-2.0.0.jar`.
+
+Then simply place that file in the `jars` folder of your Fiji installation, e.g
+`D:\Development\Fiji.app\jars\` or `/opt/Fiji.app/jars/`, possibly removing
+other versions of the same package from that folder - then (re-)start Fiji.
+
+If you'd prefer to use the cutting-edge version from GitHub, look into the
+[development instructions](DEVELOPMENT.md) for details.
+
+### Installation Testing
+
+To check the package's correct installation in Fiji, search for *Script
+Interpreter* in the Search bar, and type `:lang python`, followed by e.g.
+`import imcflibs.imagej.misc`. If no errors are shown, the installation was
+successful. Alternatively, you can scroll in the sidebar of the Interpreter to
+search for imcflibs.
+
 ## Example usage
 
 ### Shading correction / projection
@@ -50,17 +103,17 @@ correct_and_project(raw_image, out_path, model, "Maximum", ".ics")
 
 ### Split TIFFs by channels and slices
 
-* See the [Split_TIFFs_By_Channels_And_Slices.py][script_split] script.
+- See the [Split_TIFFs_By_Channels_And_Slices.py][script_split] script.
 
 ### Use status and progress bar updates
 
-* See the [FluoView_OIF_OIB_OIR_Simple_Stitcher.py][script_fvstitch] script.
+- See the [FluoView_OIF_OIB_OIR_Simple_Stitcher.py][script_fvstitch] script.
 
 [imcf]: https://www.biozentrum.unibas.ch/imcf
-[imagej]: https://imagej.net
+[imagej2]: https://imagej.net
 [fiji]: https://fiji.sc
 [jython3]: https://www.jython.org/jython-3-roadmap
-[sj_maven]: https://maven.scijava.org/#nexus-search;gav~ch.unibas.biozentrum.imcf~~~~
+[sj_maven]: https://maven.scijava.org/service/rest/repository/browse/releases/ch/unibas/biozentrum/imcf/
 [imcf_updsite]: https://imagej.net/list-of-update-sites/
 [script_split]: https://github.com/imcf/imcf-fiji-scripts/blob/master/src/main/resources/scripts/Plugins/IMCF_Utilities/Convert/Split_TIFFs_By_Channels_And_Slices.py
 [script_fvstitch]: https://github.com/imcf/imcf-fiji-scripts/blob/master/src/main/resources/scripts/Plugins/IMCF_Utilities/Stitching_Registration/FluoView_OIF_OIB_OIR_Simple_Stitcher.py

TESTING.md

@@ -1,14 +1,14 @@
 # Testing 🧪🧫 in Fiji / ImageJ2
 
-## Using `pytest` 🐍🔬 and Python 3 for plain Python code
+## Using pytest 🐍🔬 and Python 3 for plain Python code
 
 Those parts of the package that do not interact / depend on ImageJ objects can
 be tested via [`pytest`][pytest] up to a certain level, some (most?) of them
 should even work in a Python 3 environment.
 
-To perform those tests, the packges otherwise provided by ImageJ need to be
-mocked using the `imcf-fiji-mocks` package. For seting up a *venv* use the steps
-described here:
+To perform those tests, the packages otherwise provided by ImageJ need to be
+mocked using the `imcf-fiji-mocks` package. For setting up a *venv* use the
+steps described here:
 
 ```bash
 # check if we're "inside" the repo already, otherwise clone it here:
@@ -44,7 +44,7 @@ specific tests, use e.g.
 pytest tests/bdv/test_processingoptions.py
 ```
 
-## Using `pytest` 🐍🔬 and Python 2 for plain Python code
+## Using pytest 🐍🔬 and Python 2 for plain Python code
 
 For running [`pytest`][pytest] in a C-Python 2 environment, things are slightly
 more complicated than the approach described for Python 3 above as `pip` for
@@ -84,7 +84,7 @@ some basic, semi-interactive tests the following conventions are being used:
 * Any *interactive* test script should start with a header similar to the one
   described below. Paths to input data *inside* the test scripts **has** to be
   relative to the location of the `sample-data` repository mentioned above. This
-  will allow for a fairly okayish testing workflow like this:
+  will allow for a fairly okay-ish testing workflow like this:
   * Make your changes in VS Code, then trigger a build by pressing `Shift` +
   `Ctrl` + `B`. If things are configured as described in the *DEVELOPMENT*
   document, the resulting `.jar` file will be automatically placed in Fiji's