Dev bilayers (#4)

* Extend to read bilayers yaml

* Add output types

* Revert outputparam change, add zarr types to format

* Extend outputs as outputs must contain these options

* Extend format and sub_type format

* Add docker type

* Add value-choices to base model

* Add output_dir_set for params

* Add computed fields for requires_zarr and requires_plate

* Add optional advanced mode and value choice labels

* Add other input support

* Add file attachment support

* Add file_count for outputs

* Update README

* Github for version and pypi

* Expand github actions to more tests and package

* Some encoding for cli results

* Change versioning of schema

---------

Co-authored-by: Joost de Folter <folterj@gmail.com>

Author: TorecLuik

.github/workflows/python-publish.yml

@@ -0,0 +1,41 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - uses: prefix-dev/setup-pixi@v0.8.0
+      with:
+        pixi-version: latest
+      env:
+        SETUPTOOLS_SCM_PRETEND_VERSION: ${{ github.ref_name }}
+    - name: Build package
+      env:
+        SETUPTOOLS_SCM_PRETEND_VERSION: ${{ github.ref_name }}
+      run: pixi run build-package
+    - name: Generate JSON schema
+      run: pixi run json-schema > biomero-schema.json
+    - name: Upload schema to release
+      env:
+        GH_TOKEN: ${{ github.token }}
+      run: gh release upload ${{ github.ref_name }} biomero-schema.json --clobber
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -0,0 +1,23 @@
+name: Tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: windows-latest
+    env:
+      PYTHONUTF8: "1"
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: prefix-dev/setup-pixi@v0.8.0
+        with:
+          pixi-version: latest
+      - run: pixi run test
+      - run: pixi run test-validate
+      - run: pixi run test-parse
+      - run: pixi run test-pparse
+      - run: pixi run test-jparse

.gitignore

@@ -177,7 +177,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # Ruff stuff:
 .ruff_cache/

README.md

@@ -100,23 +100,23 @@ schema =
 {
   "name": "string",                      // Required. GitHub workflow repository name (without prefix). E.g. NucleiTracking-ImageJ
   "description": "string"                // Required. Description of workflow.
-  "schema-version": "string"             // Required. Semver of schema version.
+  "schema-version": "string"             // Required. Schema format identifier. Use the current schema version constant, e.g. "biomero-0.1".
   "authors":                             // Optional. Authors list.
     [
       {
         "name": "string",                // Required. Full name of author.
-        "email": "optional",             // Optional. Email address of author.
-        "affiliations": "string[]"       // Optional. List of affiliations matching "id" of an instituttion in instititions list.
+        "email": "string",               // Optional. Email address of author.
+        "affiliations": "string[]"       // Optional. List of affiliations matching "id" of an institution in institutions list.
       }
     ],
   "institutions":                        // Optional. Institutions list.
     [
       {
         "id": "string",                  // Required. Unique institute identifier.
-        "name": "string"                 // Optional. Name of the institions. Defaults to id.
+        "name": "string"                 // Optional. Name of the institution. Defaults to id.
       }
     ],
-  "citations":                           // Optional. List of citations for the tool. Defaults to empty list.
+  "citations":                           // Required. List of citations for the tool. At least one citation required.
     [
       {
         "name": "string",                // Required. Name of the tool being cited.
@@ -127,16 +127,16 @@ schema =
     ],
   // corresponding to: https://neubias-wg5.github.io/problem_class_ground_truth.html#steps-section
   "problem-class":                       // Optional. Biaflows problem class ("object-segmentation" | "pixel-classification" | "object-counting" | "object-detection" | "filament-tree-tracing" | "filament-networks-tracing" | "landmark-detection" | "particle-tracking" | "object-tracking").
-  "container-image":                     // Required. Base cotnainer description.
+  "container-image":                     // Required. Base container description.
     {
       "image": "string",                 // Required. Image to match the name of your workflow GitHub repository (lower case only). E.g. neubiaswg5/w_nucleitracking-imagej:1.0.0
-      "type": "string",                  // Required. "oci" | "singularity" (lower case only).
+      "type": "string",                  // Required. "oci" | "singularity" | "docker" (lower case only).
       "platforms": "string"[]            // Optional. Build-time multi-platform targets.
     },
   "configuration":                       // Optional. Technical configuration.
   {
     "input_folder": "string",            // Optional. Full path where the input folder must be mounted in the container. Defaults to "/inputs".
-    "output_folder": "string",           // Optional. Full path where teh output folder must be mounted in the container. Defaults to "/outputs".
+    "output_folder": "string",           // Optional. Full path where the output folder must be mounted in the container. Defaults to "/outputs".
     "resources":                         // Optional.
       {
         "networking": "boolean",         // Optional. Whether internet connection is needed. Defaults to False.
@@ -158,14 +158,22 @@ schema =
         // references to "@id" get the value of "id" in lowercase
         // references to "@ID" get the value of "id" in uppercase
         "id": "string",                  // Required. Unique parameter identifier.
-        "type": "string",                // Required. Data type of the parameter (Number|String|ineger|flaot|boolean|string|file|image|array).
-        "name": "string",                // Optional. Human-readable display name appearing in BIAFLOWS UI (paramater dialog box). Defaults to "@id".
-        "description": "string",         // Optional. Description of paramater. Context help in BIAFLOWS UI (paramater dialog box). Soft Defaults to "".
+        "type": "string",                // Required. Data type of the parameter (Number|String|integer|float|boolean|string|file|image|array|measurement|executable).
+        "name": "string",                // Optional. Human-readable display name appearing in BIAFLOWS UI (parameter dialog box). Defaults to "@id".
+        "description": "string",         // Optional. Description of parameter. Context help in BIAFLOWS UI (parameter dialog box). Soft Defaults to "".
         "value-key": "string",           // Optional. Substitution key in CLI. Defaults to "[@ID]".
         "command-line-flag": "string",   // Optional. CLI flag. Defaults to "--@id".
-        "default-value": "string|number|boolean", // Optional. Default value in BIAFLOWS UI (paramater dialog box). Soft Defaults to empty string.
+        "default-value": "string|number|boolean", // Optional. Default value in BIAFLOWS UI (parameter dialog box). Soft Defaults to empty string.
         "optional": "boolean",           // Optional. If true, parameter not required. Soft Defaults to False.
         "set-by-server": "boolean",      // Optional. If true, parameter is server-assigned. Soft Defaults to False.
+        "value-choices": "array",        // Optional. List of allowed values for this parameter.
+        "value-choices-labels": "string[]", // Optional. Display labels for value-choices, index-aligned. When null, value is used as label.
+        "mode": "string",                // Optional. UI display mode — "beginner" | "advanced". Advanced params are collapsed by default in the UI.
+        "file-count": "string",          // Optional. For file-type inputs: "single" | "multiple".
+        "format": "string|string[]",      // Optional. Type-specific. File extension(s) — see file/image/array sections below.
+        "sub-type": "string|string[]",   // Optional. Type-specific. Image sub-type(s) — see image section below.
+        "output-dir-set": "boolean",     // Optional. If true, this parameter specifies the output directory. Biomero will supply the data/out path.
+        "file-attachment": "boolean",    // Optional. If true, this is a user-supplied OMERO file-attachment input (annotation ID). Biomero will download the file from OMERO and transfer it to the HPC at runtime, then inject the resolved path as the CLI argument.
       }
     ]
   "outputs":                           // Optional. List of output parameter descriptors.
@@ -174,32 +182,45 @@ schema =
         // references to "@id" get the value of "id" in lowercase
         // references to "@ID" get the value of "id" in uppercase
         "id": "string",                  // Required. Unique parameter identifier.
-        "type": "string",                // Required. Data type of the parameter (Number|String).
-        "name": "string",                // Optional. Human-readable display name appearing in BIAFLOWS UI (paramater dialog box). Defaults to "@id".
-        "description": "string",         // Optional. Description of paramater. Context help in BIAFLOWS UI (paramater dialog box). Soft Defaults to "".
+        "type": "string",                // Required. Data type of the parameter (Number|String|integer|float|boolean|string|file|image|array|measurement|executable).
+        "name": "string",                // Optional. Human-readable display name appearing in BIAFLOWS UI (parameter dialog box). Defaults to "@id".
+        "description": "string",         // Optional. Description of parameter. Context help in BIAFLOWS UI (parameter dialog box). Soft Defaults to "".
         "value-key": "string",           // Optional. Substitution key in CLI. Defaults to "[@ID]".
         "command-line-flag": "string",   // Optional. CLI flag. Defaults to "--@id".
-        "default-value": "string|number|boolean", // Optional. Default value in BIAFLOWS UI (paramater dialog box). Soft Defaults to empty string.
+        "default-value": "string|number|boolean", // Optional. Default value in BIAFLOWS UI (parameter dialog box). Soft Defaults to empty string.
         "optional": "boolean",           // Optional. If true, parameter not required. Soft Defaults to False.
         "set-by-server": "boolean",      // Optional. If true, parameter is server-assigned. Soft Defaults to False.
+        "value-choices": "array",        // Optional. List of allowed values for this parameter.
+        "value-choices-labels": "string[]", // Optional. Display labels for value-choices, index-aligned. When null, value is used as label.
+        "mode": "string",                // Optional. UI display mode — "beginner" | "advanced". Advanced params are collapsed by default in the UI.
+        "file-count": "string",          // Optional. For file-type outputs: "single" | "multiple".
+        "format": "string|string[]",      // Optional. Type-specific. File extension(s) — see file/image/array sections below.
+        "sub-type": "string|string[]",   // Optional. Type-specific. Image sub-type(s) — see image section below.
       }
     ]
   "command-line": "string"               // Required. e.g. "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE IJ_RADIUS IJ_THRESHOLD".
 }
 
 file =
 {
-  "format": "string"                    // Required. Extension of the file type (.csv).
+  "format": "string"                    // Optional. Extension of the file type (e.g. .csv).
 }
 
 image =
 {
-  "sub-type": "string",                 // Required. Image type (grayscale|color|binary|labeled|class).
-  "format": "string"                    // Required. Extension of the image type (tif, png, jpg, jpeg, tiff, ometiff).
+  "sub-type": "string|string[]",        // Optional. Image type (grayscale|color|binary|labeled|class|plate). Can be a single value or list.
+  "format": "string|string[]"           // Optional. Extension of the image type (tif|png|jpg|jpeg|tiff|ometiff|zarr|omezarr|ome.zarr|ome-zarr). Can be a single value or list.
 }
 
 array =
 {
-  "format": "string"                    // Required. Extension of the file type (npy, npz)
+  "format": "string"                    // Optional. Extension of the file type (npy, npz)
 }
 ```
+
+## Computed Fields
+
+The following fields are automatically computed from the schema and included in the JSON output:
+
+- **`requires-zarr`** (`boolean`): `true` when any image input uses a ZARR format (`zarr`, `omezarr`, `ome.zarr`, `ome-zarr`) or has `plate` sub-type.
+- **`requires-plate`** (`boolean`): `true` when any image input has `plate` sub-type.