driftlessmap 1.1.0__tar.gz → 1.4.0__tar.gz

{driftlessmap-1.1.0 → driftlessmap-1.4.0}/CITATION.cff

@@ -4,7 +4,7 @@ message: >-
   HERBS paper listed under references.
 title: DriftlessMap
 type: software
-version: 1.1.0
+version: 1.4.0
 authors:
   - name: Mohebi & Associates
     website: https://www.mohebi-associates.org/

{driftlessmap-1.1.0 → driftlessmap-1.4.0}/MANIFEST.in

@@ -25,6 +25,8 @@ include driftlessmap/data/atlas_labels.pkl
 # Included are: icons/, data/, qss/
 recursive-include driftlessmap/icons *.svg
 recursive-include driftlessmap/icons *.png
+recursive-include driftlessmap/icons *.ico
+recursive-include driftlessmap/icons *.icns
 
 recursive-include driftlessmap/qss *.qss
 

{driftlessmap-1.1.0 → driftlessmap-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: driftlessmap
-Version: 1.1.0
+Version: 1.4.0
 Summary: Interactive histology registration and brain-atlas mapping
 Author: Pearl Saldanha, Jacopo Paglia, Jonathan R. Whitlock, Mohebi & Associates, Ali Mohebi
 Author-email: Jingyi Guo Fuglstad <jingyi.g.fuglstad@gmail.com>
@@ -34,7 +34,7 @@ Requires-Dist: PyQt6<7,>=6.8
 Requires-Dist: pyqtgraph<0.15,>=0.14
 Requires-Dist: PyOpenGL<4,>=3.1.7
 Requires-Dist: superqt<0.9,>=0.8
-Requires-Dist: opencv-python<6,>=4.10
+Requires-Dist: opencv-python-headless<6,>=4.10
 Requires-Dist: numba<1,>=0.61
 Requires-Dist: numpy<3,>=2.0
 Requires-Dist: scipy<2,>=1.13
@@ -51,6 +51,8 @@ Provides-Extra: test
 Requires-Dist: pytest>=8.3; extra == "test"
 Requires-Dist: ruff>=0.9; extra == "test"
 Requires-Dist: tomli>=2; python_version < "3.11" and extra == "test"
+Provides-Extra: desktop-build
+Requires-Dist: pyinstaller<7,>=6.11; extra == "desktop-build"
 Dynamic: license-file
 
 # DriftlessMap
@@ -98,35 +100,73 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 - Safe, versioned project and object archives.
 - Support for custom compatible atlases.
 
-## Install
+## Installation
 
-DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
-3.14 in a dedicated environment is recommended for new installations.
+DriftlessMap 1.4.0 is available as a desktop application for end users and as
+a Python package for developers.
+
+### Mode 1: desktop application for end users
+
+No Python or Conda installation is required. Download the asset for your
+computer from [GitHub Releases](https://github.com/mohebi-n-associates/DriftlessMap/releases):
+
+- **Windows 64-bit:** download `DriftlessMap-1.4.0-Windows-x64.zip`, extract
+  the complete folder, and double-click `DriftlessMap.exe`. Do not move the
+  executable out of its extracted folder.
+- **macOS:** download `DriftlessMap-1.4.0-macOS.dmg`, open it, and drag
+  `DriftlessMap.app` to Applications. The application bundle includes the
+  DriftlessMap icon and all Python dependencies.
+
+Release builds are currently unsigned. If Windows SmartScreen or macOS
+Gatekeeper displays a warning, verify that the file came from the official
+release page. On macOS, Control-click the app, choose **Open**, and confirm the
+first launch. Code signing and notarization are planned for a future release.
+
+### Mode 2: Conda and pip for developers
+
+DriftlessMap supports Python 3.10–3.14 and Qt 6 through PyQt6. Python 3.14 is
+recommended for core development:
 
 ```bash
 conda create --name DriftlessMap python=3.14 -y
 conda activate DriftlessMap
 python -m pip install --upgrade pip
+git clone https://github.com/mohebi-n-associates/DriftlessMap.git
+cd DriftlessMap
+python -m pip install -e ".[test]"
+```
+
+Launch the editable installation with `driftlessmap` or
+`python -m driftlessmap`. Library users can call `driftlessmap.run()`.
+
+To use the stable PyPI package instead of an editable checkout, run:
+
+```bash
 python -m pip install driftlessmap
 ```
 
-Launch the application with any of:
+#### Check your version and upgrade
+
+Check the installed version:
 
 ```bash
-driftlessmap
-python -m driftlessmap
+python -m driftlessmap --version
 ```
 
-```python
-import driftlessmap
+Compare it against the latest stable release on
+[PyPI](https://pypi.org/project/driftlessmap/):
 
-driftlessmap.run()
+```bash
+pip index versions driftlessmap
 ```
 
-For an editable development install, clone the repository and use
-`python -m pip install -e .`.
+Upgrade to the latest stable release:
 
-### Zeiss CZI files
+```bash
+python -m pip install --upgrade driftlessmap
+```
+
+#### Zeiss CZI files
 
 CZI support uses the optional `aicspylibczi` package, whose prebuilt packages
 currently support Python through 3.13:
@@ -138,6 +178,13 @@ python -m pip install --upgrade pip
 python -m pip install "driftlessmap[czi]"
 ```
 
+#### Building the desktop applications
+
+Native applications must be built on their target operating system. The
+release workflow builds both platforms automatically; maintainers can also run
+`packaging/build_windows.ps1` on Windows or `packaging/build_macos.sh` on
+macOS. Outputs are written to `dist/` as a Windows ZIP and a macOS DMG.
+
 ## Compatibility with HERBS
 
 The rebrand is designed not to strand existing research data:

{driftlessmap-1.1.0 → driftlessmap-1.4.0}/README.md

@@ -43,35 +43,73 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 - Safe, versioned project and object archives.
 - Support for custom compatible atlases.
 
-## Install
+## Installation
 
-DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
-3.14 in a dedicated environment is recommended for new installations.
+DriftlessMap 1.4.0 is available as a desktop application for end users and as
+a Python package for developers.
+
+### Mode 1: desktop application for end users
+
+No Python or Conda installation is required. Download the asset for your
+computer from [GitHub Releases](https://github.com/mohebi-n-associates/DriftlessMap/releases):
+
+- **Windows 64-bit:** download `DriftlessMap-1.4.0-Windows-x64.zip`, extract
+  the complete folder, and double-click `DriftlessMap.exe`. Do not move the
+  executable out of its extracted folder.
+- **macOS:** download `DriftlessMap-1.4.0-macOS.dmg`, open it, and drag
+  `DriftlessMap.app` to Applications. The application bundle includes the
+  DriftlessMap icon and all Python dependencies.
+
+Release builds are currently unsigned. If Windows SmartScreen or macOS
+Gatekeeper displays a warning, verify that the file came from the official
+release page. On macOS, Control-click the app, choose **Open**, and confirm the
+first launch. Code signing and notarization are planned for a future release.
+
+### Mode 2: Conda and pip for developers
+
+DriftlessMap supports Python 3.10–3.14 and Qt 6 through PyQt6. Python 3.14 is
+recommended for core development:
 
 ```bash
 conda create --name DriftlessMap python=3.14 -y
 conda activate DriftlessMap
 python -m pip install --upgrade pip
+git clone https://github.com/mohebi-n-associates/DriftlessMap.git
+cd DriftlessMap
+python -m pip install -e ".[test]"
+```
+
+Launch the editable installation with `driftlessmap` or
+`python -m driftlessmap`. Library users can call `driftlessmap.run()`.
+
+To use the stable PyPI package instead of an editable checkout, run:
+
+```bash
 python -m pip install driftlessmap
 ```
 
-Launch the application with any of:
+#### Check your version and upgrade
+
+Check the installed version:
 
 ```bash
-driftlessmap
-python -m driftlessmap
+python -m driftlessmap --version
 ```
 
-```python
-import driftlessmap
+Compare it against the latest stable release on
+[PyPI](https://pypi.org/project/driftlessmap/):
 
-driftlessmap.run()
+```bash
+pip index versions driftlessmap
 ```
 
-For an editable development install, clone the repository and use
-`python -m pip install -e .`.
+Upgrade to the latest stable release:
 
-### Zeiss CZI files
+```bash
+python -m pip install --upgrade driftlessmap
+```
+
+#### Zeiss CZI files
 
 CZI support uses the optional `aicspylibczi` package, whose prebuilt packages
 currently support Python through 3.13:
@@ -83,6 +121,13 @@ python -m pip install --upgrade pip
 python -m pip install "driftlessmap[czi]"
 ```
 
+#### Building the desktop applications
+
+Native applications must be built on their target operating system. The
+release workflow builds both platforms automatically; maintainers can also run
+`packaging/build_windows.ps1` on Windows or `packaging/build_macos.sh` on
+macOS. Outputs are written to `dist/` as a Windows ZIP and a macOS DMG.
+
 ## Compatibility with HERBS
 
 The rebrand is designed not to strand existing research data:

{driftlessmap-1.1.0 → driftlessmap-1.4.0}/WhatsNew.md

@@ -3,6 +3,85 @@
 This cumulative release history is maintained as a single document. New
 releases are added at the top; earlier release notes remain below them.
 
+## DriftlessMap 1.4.0
+
+Release date: 27 August 2026
+
+This release adds native desktop distribution for Windows and macOS. Official
+GitHub releases can now include a Windows ZIP containing `DriftlessMap.exe` and
+a macOS DMG containing `DriftlessMap.app`, built reproducibly on native GitHub
+Actions runners with PyInstaller. Both bundles include the application runtime,
+optional CZI support, and a new DriftlessMap application icon.
+
+The running version is now visible in both the main-window title and the
+dashboard status bar, and the application exposes its name, version,
+organization, and icon through Qt desktop metadata. The README and manual now
+separate the no-Python desktop installation intended for end users from the
+Conda/pip workflow intended for developers.
+
+---
+
+## DriftlessMap 1.3.0
+
+Release date: 27 August 2026
+
+This release makes project persistence suitable for reproducible scientific
+work. Projects now record software/schema metadata, relative and absolute path
+hints, SHA-256 identities for source histology and processed atlas resources,
+complete registration topology, complete probe-planning state, and all object
+pieces and merged objects.
+
+The exact active histology raster remains embedded in every project and can be
+restored when the original source has moved. **Save Portable Project** also
+packages the original histology source for multi-scene or future reprocessing
+work. Processed volume atlases remain external to avoid very large duplicate
+archives, but they are verified before use and can be relocated interactively.
+
+Object files now carry atlas and coordinate-frame provenance. The former Save
+Object/Load Objects wording is now Export Object/Import Objects to clarify that
+objects are already included in a project. Standalone `.dmapprobe` save/load is
+implemented for probe geometry, face, multi-probe offsets, and merge choices.
+
+---
+
+## DriftlessMap 1.2.0
+
+Release date: 27 July 2026
+
+This release adds a versioned probe-localization export designed for
+downstream electrophysiology and NWB workflows.
+
+### Probe-localization export schema 2
+
+The **Export probe localization files** action now creates four companion
+files:
+
+- `_contacts.csv` contains physical probe contacts, ordered deepest to
+  shallowest, with atlas coordinates and anatomical assignments.
+- `_track.csv` contains labeled samples along the fitted centerline, ordered
+  from insertion to tip and spaced no farther apart than one atlas voxel. This
+  is the appropriate input for localizing continuously estimated unit depths.
+- `_trajectory.csv` records insertion, tip, angles, fit quality, atlas and
+  coordinate-system metadata, export schema, software version, and the
+  probe-model tip-to-contact offset.
+- `_regions.csv` summarizes region IDs, names, acronyms, contact totals, and
+  reconstructed path lengths.
+
+Track samples include distance from insertion and tip, atlas-space
+coordinates, and the structure ID, acronym, and name at each point. For
+recognized Allen CCFv3 atlases, the export includes Allen voxel coordinates
+and physical coordinates alongside the existing explicitly qualified
+estimated Bregma values.
+
+### Upgrade notes
+
+Downstream tools that assign unit locations should require schema 2 and use
+the track table rather than inferring region boundaries from the contact or
+region summaries. Re-merge probes saved by older versions to generate the
+complete reconstruction and export metadata.
+
+---
+
 ## DriftlessMap 1.1.0
 
 Release date: 27 July 2026