pypsbuilder 2.6.4__tar.gz → 2.6.6__tar.gz

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/.github/workflows/release.yml

@@ -13,20 +13,20 @@ jobs:
 
     permissions:
       id-token: write # IMPORTANT: mandatory for trusted publishing
+      contents: read
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
         with:
           persist-credentials: false
+
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install build
+          python-version: "3.12"
+
       - name: Build package
-        run: python -m build
+        run: uv build
+
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        run: uv publish

pypsbuilder-2.6.6/.github/workflows/testing.yml

@@ -0,0 +1,45 @@
+name: Python testing
+
+on:
+  push:
+    branches:
+      - "**"
+  pull_request:
+
+jobs:
+  build:
+    name: Package testing
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+
+    env:
+      QT_QPA_PLATFORM: offscreen
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v7
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+
+      - name: Install Qt runtime dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libegl1 libxkbcommon0
+
+      - name: Install the project
+        run: uv sync --extra pyqt6 --extra tests
+
+      - name: Run Python tests
+        run: uv run pytest --cov --cov-branch --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v7
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: ondrolexa/pypsbuilder

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/.github/workflows/testrelease.yml

@@ -14,11 +14,11 @@ jobs:
       id-token: write # IMPORTANT: mandatory for trusted publishing
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
         with:
           persist-credentials: false
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: "3.x"
       - name: Install dependencies

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/.gitignore

@@ -64,3 +64,6 @@ target/
 
 # venv
 .venv/
+
+# uv lockfile (not committed for library project)
+uv.lock

pypsbuilder-2.6.6/.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+default_stages: [pre-commit, pre-push]
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.4
+    hooks:
+    - id: ruff-check
+      args: [--fix]
+      exclude: ^(venv/|docs/)
+      types: ['python']
+    - id: ruff-format
+      exclude: ^(venv/|docs/)
+      types: ['python']
+  - repo: local
+    hooks:
+    - id: pytest
+      name: pytest
+      entry: uv run pytest
+      language: system
+      types: [python]
+      pass_filenames: false
+      always_run: true

pypsbuilder-2.6.6/.readthedocs.yaml

@@ -0,0 +1,27 @@
+#.readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.com/platform/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+build:
+  os: ubuntu-26.04
+  tools:
+    python: "3.13"
+
+# Install pypsbuilder with its docs extra via uv, matching the project's
+# uv-based dev workflow (see README.md).
+python:
+  install:
+    - method: uv
+      path: .
+      extras:
+        - docs

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/CHANGELOG.md

@@ -1,6 +1,25 @@
 # Changelog
 All notable pypsbuilder changes.
 
+## [2.6.6] - 2026-08-29
+### Fixed
+ - project extra jupyter renamed to lab
+
+ ## [2.6.5] - 2026-08-29
+### Added
+ - `Import from JSON` menu item in ptbuilder/txbuilder/pxbuilder to batch-import invariant points and univariant lines JSON
+ - THERMOCALC 3.51 support in `tcinit`
+### Fixed
+ - security: project files now load through a restricted unpickler, closing an arbitrary-code-execution risk from opening a crafted `.ptb`/`.txb`/`.pxb` file
+ - `eval_expr` now supports unary +/- (e.g. `-mode`)
+ - fixed crash opening some real project files (`annotate()` got an array instead of a scalar)
+ - `PS.show_grid` no longer silently drops its `expr`/`interpolation` arguments
+ - fixed `PXPS.fix_solutions` not reseeding THERMOCALC guesses from a solved neighbor before retrying a failed grid point
+ - THERMOCALC/drawpd subprocess calls no longer hang indefinitely on an unresponsive process
+ - fixed deprecated matplotlib colormap API usage
+### Changed
+ - faster diagram field lookups and grid calculation via spatial indexing and vectorized nearest-point search
+
 ## [2.6.4] - 2025-08-03
 ### Fixed
  - TC 3.51 compatibility added

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/CONTRIBUTING.md

@@ -50,8 +50,9 @@ Ready to contribute? Here's how to set up `pypsbuilder` for local development.
 
 1. Just head over to the [GitHub page](https://github.com/ondrolexa/pypsbuilder) and click the "Fork" button. It's just that simple. Once you've done that, you can use your favorite git client to clone your repo.
 
-2. Create a branch for local development
+2. Set up a development environment with [uv](https://docs.astral.sh/uv/) and create a branch for local development. See the "Contributing / development install" section in [README.md](README.md) for the full command reference (running tests, formatting/linting with ruff, pre-commit hooks).
 ```
+    $ uv sync --group dev
     $ git checkout -b name-of-your-bugfix-or-feature
 ```
    Now you can make your changes locally.
@@ -70,4 +71,4 @@ Before you submit a pull request, check that it meets these guidelines.
 
 1. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
+   feature to the list in README.md.

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: pypsbuilder
-Version: 2.6.4
+Version: 2.6.6
 Summary: THERMOCALC front-end for constructing and analyzing PT pseudosections
 Project-URL: Homepage, https://github.com/ondrolexa/pypsbuilder
 Project-URL: Documentation, https://pypsbuilder.readthedocs.io
@@ -37,11 +37,9 @@ Keywords: THERMOCALC,petrology
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Utilities
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Requires-Dist: matplotlib>=3.8
 Requires-Dist: networkx
 Requires-Dist: numpy
@@ -50,21 +48,12 @@ Requires-Dist: scikit-image
 Requires-Dist: scipy
 Requires-Dist: shapely>=2
 Requires-Dist: tqdm
-Provides-Extra: dev
-Requires-Dist: black; extra == 'dev'
-Requires-Dist: jupyterlab; extra == 'dev'
-Requires-Dist: pyqt6; extra == 'dev'
-Requires-Dist: pytest; extra == 'dev'
-Requires-Dist: pytest-cov; extra == 'dev'
-Requires-Dist: sphinx; extra == 'dev'
-Requires-Dist: sphinx-mdinclude; extra == 'dev'
-Requires-Dist: sphinx-rtd-theme; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == 'docs'
 Requires-Dist: sphinx-mdinclude; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme; extra == 'docs'
-Provides-Extra: jupyter
-Requires-Dist: jupyterlab; extra == 'jupyter'
+Provides-Extra: lab
+Requires-Dist: jupyterlab; extra == 'lab'
 Provides-Extra: pyqt5
 Requires-Dist: pyqt5; extra == 'pyqt5'
 Provides-Extra: pyqt6
@@ -78,12 +67,28 @@ Description-Content-Type: text/markdown
 
 [![PyPI - Version](https://img.shields.io/pypi/v/pypsbuilder)](https://pypi.org/project/pypsbuilder/)
 [![Testing](https://github.com/ondrolexa/pypsbuilder/actions/workflows/testing.yml/badge.svg?event=push)](https://github.com/ondrolexa/pypsbuilder)
-[![Documentation Status](https://readthedocs.org/projects/polylx/badge/?version=stable)](https://pypsbuilder.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/pypsbuilder/badge/?version=latest)](https://pypsbuilder.readthedocs.io/en/latest/?badge=latest)
 
 Not that simplistic THERMOCALC front-end for constructing and visualizations of P-T, T-X and P-X pseudosections
 
 ## How to install
 
+### Using uv (recommended)
+
+If you don't already have [uv](https://docs.astral.sh/uv/) installed, see the
+[installation instructions](https://docs.astral.sh/uv/getting-started/installation/).
+
+Create an isolated environment and install **pypsbuilder** into it. **You should choose the UI framework using option** `pyqt5` **or** `pyqt6`:
+
+    uv venv
+    uv pip install pypsbuilder[pyqt6]
+
+JupyterLab could also be installed providing the `lab` option:
+
+    uv pip install pypsbuilder[pyqt6,lab]
+
+### Using pip and venv
+
 It is strongly suggested to install **pypsbuilder** into separate environment. You can create
 Python virtual environment. For Linux and macOS use:
 
@@ -111,9 +116,9 @@ and install **pypsbuilder** using pip within the environment. **You should choos
 
     pip install pypsbuilder[pyqt6]
 
-JupyterLab could also be installed providing the `jupyter` option:
+JupyterLab could also be installed providing the `lab` option:
 
-    pip install pypsbuilder[pyqt6,jupyter]
+    pip install pypsbuilder[pyqt6,lab]
 
 ## I'm using conda or mamba to manage environments
 
@@ -143,15 +148,61 @@ and install with pip. As PyQt is already installed with mamba/conda, we will ins
 > pip install --no-deps pypsbuilder
 > ```
 
-#### Upgrade existing installation
+### Upgrade existing installation
 
 To upgrade an already installed **pypsbuilder** to the latest release:
 
-    pip install --upgrade pypsbuilder
+    uv pip install --upgrade pypsbuilder[pyqt6]
+
+## Contributing / development install
+
+Clone the repository and install with uv:
+
+    uv sync --group dev
+
+This installs pypsbuilder in editable mode with UI, notebook, test and docs
+extras plus dev tooling (ruff, pre-commit).
+
+### Running tests
+
+Run the full test suite (must be run from the repo root, since tests
+reference `./examples/outputs` with a relative path):
+
+    uv run pytest
+    uv run pytest --cov --cov-report=xml
+
+Run a single test:
+
+    uv run pytest pypsbuilder/tests/test_pclasses.py::test_parse_ini1
+
+### Formatting and linting
+
+pypsbuilder uses [ruff](https://docs.astral.sh/ruff/) for both formatting and linting:
+
+    uv run ruff format pypsbuilder
+    uv run ruff check pypsbuilder
+
+### pre-commit hooks
+
+Formatting, linting and the test suite also run automatically via
+[pre-commit](https://pre-commit.com/):
+
+    uv run pre-commit install
+    uv run pre-commit run --all-files
+
+### Building the package
+
+    uv build
+
+### Rebuilding Qt UI modules
+
+After editing a `.ui` file in Qt Designer, regenerate the corresponding
+`ui_*.py` module (requires `pyuic6`):
 
-or to the latest master version:
+    cd pypsbuilder/ui && ./compile_ui.sh
 
-    pip install --upgrade https://github.com/ondrolexa/pypsbuilder/archive/master.zip
+The script rewrites each generated file's `PyQt6` imports to `qtpy`
+imports, so the app stays usable with either `pyqt5` or `pyqt6`.
 
 ## Documentation and tutorials
 

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/README.md

@@ -2,12 +2,28 @@
 
 [![PyPI - Version](https://img.shields.io/pypi/v/pypsbuilder)](https://pypi.org/project/pypsbuilder/)
 [![Testing](https://github.com/ondrolexa/pypsbuilder/actions/workflows/testing.yml/badge.svg?event=push)](https://github.com/ondrolexa/pypsbuilder)
-[![Documentation Status](https://readthedocs.org/projects/polylx/badge/?version=stable)](https://pypsbuilder.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/pypsbuilder/badge/?version=latest)](https://pypsbuilder.readthedocs.io/en/latest/?badge=latest)
 
 Not that simplistic THERMOCALC front-end for constructing and visualizations of P-T, T-X and P-X pseudosections
 
 ## How to install
 
+### Using uv (recommended)
+
+If you don't already have [uv](https://docs.astral.sh/uv/) installed, see the
+[installation instructions](https://docs.astral.sh/uv/getting-started/installation/).
+
+Create an isolated environment and install **pypsbuilder** into it. **You should choose the UI framework using option** `pyqt5` **or** `pyqt6`:
+
+    uv venv
+    uv pip install pypsbuilder[pyqt6]
+
+JupyterLab could also be installed providing the `lab` option:
+
+    uv pip install pypsbuilder[pyqt6,lab]
+
+### Using pip and venv
+
 It is strongly suggested to install **pypsbuilder** into separate environment. You can create
 Python virtual environment. For Linux and macOS use:
 
@@ -35,9 +51,9 @@ and install **pypsbuilder** using pip within the environment. **You should choos
 
     pip install pypsbuilder[pyqt6]
 
-JupyterLab could also be installed providing the `jupyter` option:
+JupyterLab could also be installed providing the `lab` option:
 
-    pip install pypsbuilder[pyqt6,jupyter]
+    pip install pypsbuilder[pyqt6,lab]
 
 ## I'm using conda or mamba to manage environments
 
@@ -67,15 +83,61 @@ and install with pip. As PyQt is already installed with mamba/conda, we will ins
 > pip install --no-deps pypsbuilder
 > ```
 
-#### Upgrade existing installation
+### Upgrade existing installation
 
 To upgrade an already installed **pypsbuilder** to the latest release:
 
-    pip install --upgrade pypsbuilder
+    uv pip install --upgrade pypsbuilder[pyqt6]
+
+## Contributing / development install
+
+Clone the repository and install with uv:
+
+    uv sync --group dev
+
+This installs pypsbuilder in editable mode with UI, notebook, test and docs
+extras plus dev tooling (ruff, pre-commit).
+
+### Running tests
+
+Run the full test suite (must be run from the repo root, since tests
+reference `./examples/outputs` with a relative path):
+
+    uv run pytest
+    uv run pytest --cov --cov-report=xml
+
+Run a single test:
+
+    uv run pytest pypsbuilder/tests/test_pclasses.py::test_parse_ini1
+
+### Formatting and linting
+
+pypsbuilder uses [ruff](https://docs.astral.sh/ruff/) for both formatting and linting:
+
+    uv run ruff format pypsbuilder
+    uv run ruff check pypsbuilder
+
+### pre-commit hooks
+
+Formatting, linting and the test suite also run automatically via
+[pre-commit](https://pre-commit.com/):
+
+    uv run pre-commit install
+    uv run pre-commit run --all-files
+
+### Building the package
+
+    uv build
+
+### Rebuilding Qt UI modules
+
+After editing a `.ui` file in Qt Designer, regenerate the corresponding
+`ui_*.py` module (requires `pyuic6`):
 
-or to the latest master version:
+    cd pypsbuilder/ui && ./compile_ui.sh
 
-    pip install --upgrade https://github.com/ondrolexa/pypsbuilder/archive/master.zip
+The script rewrites each generated file's `PyQt6` imports to `qtpy`
+imports, so the app stays usable with either `pyqt5` or `pyqt6`.
 
 ## Documentation and tutorials
 

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/docs/api/pypsbuilder.psclasses.TCResult.rst

@@ -15,6 +15,7 @@
    
       ~TCResult.__init__
       ~TCResult.from_block
+      ~TCResult.from_block351
       ~TCResult.rename_phase
    
    

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/docs/api/pypsbuilder.psexplorer.PXPS.rst

@@ -41,7 +41,6 @@
       ~PXPS.merge_data
       ~PXPS.onclick
       ~PXPS.overlap_isopleths
-      ~PXPS.pointcalc
       ~PXPS.remove_grid_data
       ~PXPS.save
       ~PXPS.save_tab

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/docs/api/pypsbuilder.psexplorer.TXPS.rst

@@ -41,7 +41,6 @@
       ~TXPS.merge_data
       ~TXPS.onclick
       ~TXPS.overlap_isopleths
-      ~TXPS.pointcalc
       ~TXPS.remove_grid_data
       ~TXPS.save
       ~TXPS.save_tab

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/docs/api/pypsbuilder.tcapi.TC34API.rst

@@ -5,14 +5,14 @@
 
 .. autoclass:: TC34API
 
-
+   
    .. automethod:: __init__
 
-
+   
    .. rubric:: Methods
 
    .. autosummary::
-
+   
       ~TC34API.__init__
       ~TC34API.calc_assemblage
       ~TC34API.calc_p
@@ -31,15 +31,15 @@
       ~TC34API.rundr
       ~TC34API.runtc
       ~TC34API.update_scriptfile
+   
+   
 
-
-
-
-
+   
+   
    .. rubric:: Attributes
 
    .. autosummary::
-
+   
       ~TC34API.axfile
       ~TC34API.csvfile
       ~TC34API.dataset
@@ -52,5 +52,7 @@
       ~TC34API.ofile
       ~TC34API.prefsfile
       ~TC34API.scriptfile
-      ~TC34API.tcversionfloat
       ~TC34API.tcversion
+      ~TC34API.tcversionfloat
+   
+   

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/docs/api/pypsbuilder.tcapi.TC35API.rst

@@ -5,14 +5,14 @@
 
 .. autoclass:: TC35API
 
-
+   
    .. automethod:: __init__
 
-
+   
    .. rubric:: Methods
 
    .. autosummary::
-
+   
       ~TC35API.__init__
       ~TC35API.calc_assemblage
       ~TC35API.calc_p
@@ -24,21 +24,20 @@
       ~TC35API.dogmin
       ~TC35API.parse_dogmin
       ~TC35API.parse_logfile
-      ~TC35API.parse_logfile_backup
       ~TC35API.read_prefsfile
       ~TC35API.read_scriptfile
       ~TC35API.rundr
       ~TC35API.runtc
       ~TC35API.update_scriptfile
+   
+   
 
-
-
-
-
+   
+   
    .. rubric:: Attributes
 
    .. autosummary::
-
+   
       ~TC35API.axfile
       ~TC35API.csvfile
       ~TC35API.dataset
@@ -51,5 +50,7 @@
       ~TC35API.ofile
       ~TC35API.prefsfile
       ~TC35API.scriptfile
-      ~TC35API.tcversionfloat
       ~TC35API.tcversion
+      ~TC35API.tcversionfloat
+   
+   

{pypsbuilder-2.6.4 → pypsbuilder-2.6.6}/docs/command-line.rst

@@ -2,8 +2,9 @@ Command line scripts
 ====================
 
 Before any further calculations you can check and draw your pseudosection using
-`psshow` command which construct finished areas within your project. It has few
-options to label pseudosection with assamblages or highlight out phase lines.
+the `psshow` command, which draws the finished areas within your project. It has
+a few options to label the pseudosection with assemblages or highlight out-phase
+lines.
 
 .. parsed-literal::
 
@@ -18,9 +19,9 @@ options to label pseudosection with assamblages or highlight out phase lines.
     positional arguments:
       project               builder project file(s)
 
-    optional arguments:
+    options:
       -h, --help            show this help message and exit
-      -o OUT [OUT ...], --out OUT [OUT ...]
+      -o, --out OUT [OUT ...]
                             highlight out lines for given phases
       -l, --label           show area labels
       --origwd              use stored original working directory
@@ -61,7 +62,7 @@ aware that calculations takes some time.
     positional arguments:
       project               builder project file(s)
 
-    optional arguments:
+    options:
       -h, --help            show this help message and exit
       --nx NX               number of T steps
       --ny NY               number of P steps
@@ -95,12 +96,12 @@ Once gridded you can draw isopleths diagrams using `psiso` command:
       project               builder project file(s)
       phase                 phase used for contouring
 
-    optional arguments:
+    options:
       -h, --help            show this help message and exit
-      -e EXPR, --expr EXPR  expression evaluated to calculate values
+      -e, --expr EXPR       expression evaluated to calculate values
       -f, --filled          filled contours
       --origwd              use stored original working directory
-      -o OUT [OUT ...], --out OUT [OUT ...]
+      -o, --out OUT [OUT ...]
                             highlight out lines for given phases
       --nosplit             controls whether the underlying contour is removed or
                             not
@@ -166,3 +167,32 @@ Another example of some other options.
     --out chl ep --cmap YlGnBu_r
 
 .. image:: images/psiso_other.png
+
+Export project for drawpd
+--------------------------
+
+The `psdrawpd` command exports a project into the legacy ``drawpd`` format,
+useful for compatibility with older THERMOCALC tooling or for archiving a
+diagram outside of pypsbuilder.
+
+.. parsed-literal::
+
+    $ psdrawpd -h
+    usage: psdrawpd [-h] [-a] [--origwd] [--tolerance TOLERANCE]
+                    project [project ...]
+
+    Generate drawpd file from project
+
+    positional arguments:
+      project               psbuilder project file(s)
+
+    options:
+      -h, --help            show this help message and exit
+      -a, --areas           export also areas
+      --origwd              use stored original working directory
+      --tolerance TOLERANCE
+                            tolerance to simplify univariant lines
+
+.. parsed-literal::
+
+    $ psdrawpd '/path/to/project.ptb' -a