various docs updates

nsheff · web-flow · commit 1cf3b3826f5c · 2026-03-05T22:23:08.000-05:00
diff --git a/docs/looper/changelog.md b/docs/looper/changelog.md
@@ -2,12 +2,14 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [Unreleased]
+## [2.1.0] -- 2026-03-05
 
 ### Added
-- Added `inject_env_vars` pipeline interface property for injecting environment variables into submission scripts
-- Added `pipestat_config_required` pipeline interface property to control pipestat handoff validation
-- Added validation that pipestat-enabled interfaces (with `output_schema`) pass config to the pipeline via CLI (`{pipestat.*}`) or environment variable (`PIPESTAT_CONFIG` in `inject_env_vars`)
+- `inject_env_vars` pipeline interface property for environment variables in submission scripts
+- `pipestat_config_required` pipeline interface property for pipestat handoff validation
+
+### Changed
+- Fixed import-time logging that overrode root logger configuration
 
 ## [2.0.3] -- 2025-09-23
 ### Fixed
diff --git a/docs/pipestat/changelog.md b/docs/pipestat/changelog.md
@@ -2,6 +2,18 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.13.1] - 2026-03-05
+### Changed
+- Fixed import-time logging that overrode root logger configuration
+
+## [0.13.0] - 2026-02-25
+### Changed
+- Renamed `PipestatBoss` to `PipestatDualManager`
+- Added classmethod constructors for each backend type
+- Added `validate_results` and `additional_properties` options
+- Migrated to yacman v1 API
+- Modernized codebase: Google-style docstrings, type hints
+
 ## [0.12.2] - 2025-09-25
 ### Fixed
 - Fix setting with copy warning for pephub backend [#206](https://github.com/pepkit/pipestat/issues/206)
diff --git a/docs/pipestat/code/api-quickstart.md b/docs/pipestat/code/api-quickstart.md
@@ -38,7 +38,7 @@ print(psm.schema)
      - name_of_something : {'type': 'string', 'description': 'Name of something'}
      - switch_value : {'type': 'boolean', 'description': 'Is the switch on or off'}
      - output_file : {'description': 'This a path to the output file', 'type': 'object', 'object_type': 'file', 'properties': {'path': {'type': 'string'}, 'title': {'type': 'string'}}, 'required': ['path', 'title']}
-     - output_image : {'description': 'This a path to the output image', 'type': 'object', 'object_type': 'image', 'properties': {'path': {'type': 'string'}, 'thumbnail_path': {'type': 'string'}, 'title': {'type': 'string'}}, 'required': ['path', 'thumbnail_path', 'title']}
+     - output_image : {'description': 'This a path to the output image', 'type': 'object', 'object_type': 'image', 'properties': {'path': {'type': 'string'}, 'thumbnail_path': {'type': 'string'}, 'title': {'type': 'string'}}, 'required': ['path', 'title']}
      - md5sum : {'type': 'string', 'description': 'MD5SUM of an object', 'highlight': True}
      Status properties:
      - None
diff --git a/docs/pipestat/code/python-tutorial.md b/docs/pipestat/code/python-tutorial.md
@@ -154,7 +154,7 @@ psm.result_schemas
       'properties': {'path': {'type': 'string'},
        'thumbnail_path': {'type': 'string'},
        'title': {'type': 'string'}},
-      'required': ['path', 'thumbnail_path', 'title']},
+      'required': ['path', 'title']},
      'md5sum': {'type': 'string',
       'description': 'MD5SUM of an object',
       'highlight': True}}
diff --git a/docs/pipestat/notebooks/api-quickstart.ipynb b/docs/pipestat/notebooks/api-quickstart.ipynb
@@ -65,7 +65,7 @@
       " - name_of_something : {'type': 'string', 'description': 'Name of something'}\n",
       " - switch_value : {'type': 'boolean', 'description': 'Is the switch on or off'}\n",
       " - output_file : {'description': 'This a path to the output file', 'type': 'object', 'object_type': 'file', 'properties': {'path': {'type': 'string'}, 'title': {'type': 'string'}}, 'required': ['path', 'title']}\n",
-      " - output_image : {'description': 'This a path to the output image', 'type': 'object', 'object_type': 'image', 'properties': {'path': {'type': 'string'}, 'thumbnail_path': {'type': 'string'}, 'title': {'type': 'string'}}, 'required': ['path', 'thumbnail_path', 'title']}\n",
+      " - output_image : {'description': 'This a path to the output image', 'type': 'object', 'object_type': 'image', 'properties': {'path': {'type': 'string'}, 'thumbnail_path': {'type': 'string'}, 'title': {'type': 'string'}}, 'required': ['path', 'title']}\n",
       " - md5sum : {'type': 'string', 'description': 'MD5SUM of an object', 'highlight': True}\n",
       " Status properties:\n",
       " - None\n"
diff --git a/docs/pipestat/notebooks/python-tutorial.ipynb b/docs/pipestat/notebooks/python-tutorial.ipynb
@@ -249,7 +249,7 @@
        "  'properties': {'path': {'type': 'string'},\n",
        "   'thumbnail_path': {'type': 'string'},\n",
        "   'title': {'type': 'string'}},\n",
-       "  'required': ['path', 'thumbnail_path', 'title']},\n",
+       "  'required': ['path', 'title']},\n",
        " 'md5sum': {'type': 'string',\n",
        "  'description': 'MD5SUM of an object',\n",
        "  'highlight': True}}"
diff --git a/docs/pipestat/pipestat-schema.md b/docs/pipestat/pipestat-schema.md
@@ -22,7 +22,7 @@ Pipestat also extends the json schema vocabulary by adding two _additional_ type
     - `title`: human readable description of the file
 - `image`:
     - `path`: path to the reported image, usually PDF
-    - `thumbnail`: path to the reported thumbnail, usually PNG or JPEG
+    - `thumbnail_path` (optional): path to the reported thumbnail, usually PNG or JPEG. If not provided, falls back to `path`.
     - `title`: human readable description of the image
 
 
@@ -147,7 +147,6 @@ $defs:
         type: string
     required:
       - path
-      - thumbnail_path
       - title
   file:
     type: object
diff --git a/docs/pipestat/pipestat-specification.md b/docs/pipestat/pipestat-specification.md
@@ -37,7 +37,7 @@ Importantly, pipestat extends the jsonschema vocabulary by adding two additional
     - `title`: human readable description of the file
 - `image`:
     - `path`: path to the reported image, usually PDF
-    - `thumbnail`: path to the reported thumbnail, usually PNG or JPEG
+    - `thumbnail_path` (optional): path to the reported thumbnail, usually PNG or JPEG. If not provided, falls back to `path`.
     - `title`: human readable description of the image
 
 # Pipestat output schema
@@ -165,7 +165,6 @@ $defs:
         type: string
     required:
       - path
-      - thumbnail_path
       - title
   file:
     type: object
diff --git a/docs/pipestat/tests/data/sample_output_schema.yaml b/docs/pipestat/tests/data/sample_output_schema.yaml
@@ -43,7 +43,6 @@ $defs:
         type: string
     required:
       - path
-      - thumbnail_path
       - title
   file:
     type: object
diff --git a/docs/pypiper/changelog.md b/docs/pypiper/changelog.md
@@ -1,5 +1,31 @@
 # Changelog
 
+## [0.15.1] -- 2026-03-05
+### Changed
+- Updated for logmuse 0.3.0 compatibility
+
+## [0.15.0] -- 2026-02-13
+
+### Changed
+- Migrated from setup.py to pyproject.toml with hatchling backend
+- Replaced Black/isort with Ruff for linting and formatting
+- Updated GitHub Actions to v4/v5 with Python 3.10-3.14 CI matrix
+- Removed Python 2 compatibility code and legacy packaging files
+- Version now sourced from importlib.metadata (removed _version.py)
+- Converted all docstrings to Google-style formatting
+- Consolidated documentation into pepspec; removed local docs/ and mkdocs.yml
+- Updated README badges and documentation links
+
+### Added
+- `clean_add()` now accepts None values, enabling safe use with conditionally-assigned variables
+- Pipestat version displayed in pipeline version log output
+
+### Removed
+- Removed magic schema discovery (`default_pipestat_output_schema()`)
+
+### Improved
+- Test quality: added missing assertions, removed permanently-skipped tests, added shared fixtures
+
 ## [0.14.5] -- 2025-09-22
 ### Changed
 - Remove veracitools dependency [#233](https://github.com/databio/pypiper/issues/233)
diff --git a/docs/pypiper/features.md b/docs/pypiper/features.md
@@ -34,4 +34,4 @@ Pypiper closes pipelines gracefully on interrupt or termination signals, convert
 
 ![](img/recovery.svg) **Dynamic recovery**
 
-If a job is interrupted (with SIGINT or SIGTERM), either from a user or by a cluster resource manager, pypiper will set a `dynamic recovery` flag. The next time the run is started, it will automatically pick up where it left off. This makes pypiper pipelines `automatically pre-emption ready`, so they can be immediately deployed on servers where jobs may be pre-emptied.
+If a job is interrupted (with SIGINT or SIGTERM), either from a user or by a cluster resource manager, pypiper will set a `dynamic recovery` flag. The next time the run is started, it will automatically pick up where it left off. This makes pypiper pipelines `automatically pre-emption ready`, so they can be immediately deployed on servers where jobs may be pre-empted.
