pypsbuilder 2.4.2__tar.gz → 2.5.1__tar.gz

{pypsbuilder-2.4.2 → pypsbuilder-2.5.1}/CHANGELOG.md

@@ -1,9 +1,17 @@
 # Changelog
 All notable pypsbuilder changes.
 
+## [2.5.0] - 2024-12-13
+Fully refactored tp pyproject.toml
+
+## [2.5.0] - 2024-12-13
+### Fixed
+ - fix for coe-q
+
 ## [2.4.2] - 2024-04-23
 ### Fixed
  - another fix of and-ky-sill triple point linking
+
 ## [2.4.1] - 2024-03-07
 ### Fixed
  - fixed and-ky-sill triple point uniline suggestions
@@ -59,7 +67,7 @@ All notable pypsbuilder changes.
 - latest THERMOCALC 3.50 compatibility
 
 ### Added
-- isopleths quadratic surface fit method added 
+- isopleths quadratic surface fit method added
 - isopleths figure and savefig options added
 
 ## [2.2.2] - 2021-01-25

pypsbuilder-2.5.1/PKG-INFO

@@ -0,0 +1,95 @@
+Metadata-Version: 2.1
+Name: pypsbuilder
+Version: 2.5.1
+Summary: THERMOCALC front-end for constructing and analyzing PT pseudosections
+Home-page: https://github.com/ondrolexa/pypsbuilder
+License: MIT
+Keywords: petrology,THERMOCALC
+Author: Ondrej Lexa
+Author-email: lexa.ondrej@gmail.com
+Requires-Python: >=3.9,<4.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Utilities
+Requires-Dist: matplotlib (>=3.6,<4.0)
+Requires-Dist: networkx (>=3.2,<4.0)
+Requires-Dist: numpy (>=1.20,<2.0)
+Requires-Dist: pyqt5 (>=5.15,<6.0)
+Requires-Dist: scipy (>=1.10,<2.0)
+Requires-Dist: shapely (>=2.0,<3.0)
+Requires-Dist: tqdm (>=4.0,<5.0)
+Project-URL: Documentation, https://pypsbuilder.readthedocs.io
+Project-URL: Repository, https://github.com/ondrolexa/pypsbuilder
+Description-Content-Type: text/markdown
+
+# pypsbuilder
+
+![master](https://github.com/ondrolexa/pypsbuilder/actions/workflows/master.yml/badge.svg)
+[![Documentation Status](https://readthedocs.org/projects/pypsbuilder/badge/?version=latest)](https://pypsbuilder.readthedocs.io/en/latest/?badge=latest)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/ondrolexa/pypsbuilder/blob/master/LICENSE)
+[![GitHub release (latest by date)](https://img.shields.io/github/v/release/ondrolexa/pypsbuilder)](https://github.com/ondrolexa/pypsbuilder/releases/latest)
+[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&url=https%3A%2F%2Fgithub.com%2Fondrolexa%2Fpypsbuilder)](https://twitter.com/intent/tweet?text=Wow:&url=https%3A%2F%2Fgithub.com%2Fondrolexa%2Fpypsbuilder)
+
+Not that simplistic THERMOCALC front-end for constructing and visualizations of P-T, T-X and P-X pseudosections
+
+## How to install
+
+Easiest way to install **pypsbuilder** is to use pip:
+
+    pip install pypsbuilder
+
+or if you downloaded pypsbuilder repository, run in unzipped folder:
+
+    pip install .
+
+#### Install master version
+
+You can install latest version from master branch on GitHub:
+
+    pip install https://github.com/ondrolexa/pypsbuilder/archive/master.zip
+
+#### Upgrade existing installation
+
+To upgrade an already installed **pypsbuilder** to the latest release:
+
+    pip install --upgrade pypsbuilder
+
+or to latest master version:
+
+    pip install --upgrade https://github.com/ondrolexa/pypsbuilder/archive/master.zip
+
+### Install using conda or mamba
+
+ Create environment from the included `environment.yml` file:
+
+    conda env create -f environment.yml
+
+or
+
+    mamba env create -f environment.yml
+
+Then activate the new environment:
+
+    conda activate pyps
+
+or
+
+    mamba activate pyps
+
+## Documentation and tutorials
+
+Check documentation and tutorials on RTD [https://pypsbuilder.readthedocs.io/en/latest/](https://pypsbuilder.readthedocs.io/en/latest/)
+
+## License
+
+pypsbuilder is free software: you can redistribute it and/or modify it under the terms of the MIT License. A copy of this license is provided in ``LICENSE`` file.
+

{pypsbuilder-2.4.2 → pypsbuilder-2.5.1}/README.md

@@ -10,23 +10,7 @@ Not that simplistic THERMOCALC front-end for constructing and visualizations of
 
 ## How to install
 
-Easiest way to install **pypsbuilder** is to use conda/mamba package management system. Create environment from the included `environment.yml` file:
-
-    conda env create -f environment.yml
-
-or
-
-    mamba env create -f environment.yml
-
-Then activate the new environment:
-
-    conda activate pyps
-
-or
-
-    mamba activate pyps
-
-and install pypsbuilder using pip:
+Easiest way to install **pypsbuilder** is to use pip:
 
     pip install pypsbuilder
 
@@ -34,13 +18,13 @@ or if you downloaded pypsbuilder repository, run in unzipped folder:
 
     pip install .
 
-### Install master version
+#### Install master version
 
 You can install latest version from master branch on GitHub:
 
     pip install https://github.com/ondrolexa/pypsbuilder/archive/master.zip
 
-### Upgrade existing installation
+#### Upgrade existing installation
 
 To upgrade an already installed **pypsbuilder** to the latest release:
 
@@ -50,6 +34,24 @@ or to latest master version:
 
     pip install --upgrade https://github.com/ondrolexa/pypsbuilder/archive/master.zip
 
+### Install using conda or mamba
+
+ Create environment from the included `environment.yml` file:
+
+    conda env create -f environment.yml
+
+or
+
+    mamba env create -f environment.yml
+
+Then activate the new environment:
+
+    conda activate pyps
+
+or
+
+    mamba activate pyps
+
 ## Documentation and tutorials
 
 Check documentation and tutorials on RTD [https://pypsbuilder.readthedocs.io/en/latest/](https://pypsbuilder.readthedocs.io/en/latest/)

pypsbuilder-2.5.1/pyproject.toml

@@ -0,0 +1,68 @@
+[tool.poetry]
+name = "pypsbuilder"
+version = "2.5.1"
+description = "THERMOCALC front-end for constructing and analyzing PT pseudosections"
+authors = ["Ondrej Lexa <lexa.ondrej@gmail.com>"]
+readme = "README.md"
+license = "MIT"
+repository = "https://github.com/ondrolexa/pypsbuilder"
+documentation = "https://pypsbuilder.readthedocs.io"
+keywords = ["petrology", "THERMOCALC"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Utilities",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+include = ["AUTHORS.md", "CHANGELOG.md", "CONTRIBUTING.md"]
+
+
+[tool.poetry.dependencies]
+python = "^3.9"
+numpy = "^1.20"
+matplotlib = "^3.6"
+pyqt5 = "^5.15"
+scipy = "^1.10"
+networkx = "^3.2"
+shapely = "^2.0"
+tqdm = "^4.0"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4"
+black = "^24"
+
+[tool.poetry.scripts]
+ptbuilder = "pypsbuilder.psbuilders:ptbuilder"
+txbuilder = "pypsbuilder.psbuilders:txbuilder"
+pxbuilder = "pypsbuilder.psbuilders:pxbuilder"
+psshow = "pypsbuilder.psexplorer:ps_show"
+psiso = "pypsbuilder.psexplorer:ps_iso"
+psgrid = "pypsbuilder.psexplorer:ps_grid"
+psdrawpd = "pypsbuilder.psexplorer:ps_drawpd"
+tcinit = "pypsbuilder.tcinit:tcprojinit"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.black]
+line-length = 88
+include = '\.pyi?$'
+exclude = '''
+/(
+  \.toml
+  |\.sh
+  |\.git
+  |\.ini
+)/
+'''
+
+[[tool.poetry.source]]
+name = "pypi-public"
+url = "https://pypi.org/simple/"

{pypsbuilder-2.4.2 → pypsbuilder-2.5.1}/pypsbuilder/__init__.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 
+import importlib.metadata
 from pypsbuilder.psexplorer import PTPS, TXPS, PXPS
 from pypsbuilder.psclasses import (
     InvPoint,
@@ -22,7 +23,7 @@ __all__ = (
     "get_tcapi",
 )
 
-__version__ = "2.4.2"
+__version__ = importlib.metadata.version("pypsbuilder")
 __author__ = "Ondrej Lexa"
-__copyright__ = "© Ondrej Lexa 2024"
+__copyright__ = "© Ondrej Lexa 2016-2024"
 __email__ = "lexa.ondrej@gmail.com"

{pypsbuilder-2.4.2 → pypsbuilder-2.5.1}/pypsbuilder/psbuilders.py

@@ -1,4 +1,5 @@
 """Visual pseudosection builder for THERMOCALC."""
+
 # author: Ondrej Lexa
 # website: https://github.com/ondrolexa/pypsbuilder
 
@@ -14,7 +15,7 @@ from pathlib import Path
 from datetime import datetime
 import itertools
 
-from pkg_resources import resource_filename
+import importlib.resources as ires
 from PyQt5 import QtCore, QtGui, QtWidgets
 from PyQt5.QtCore import QT_VERSION_STR
 from PyQt5.Qt import PYQT_VERSION_STR
@@ -94,7 +95,9 @@ class BuildersBase(QtWidgets.QMainWindow):
         res = QtWidgets.QDesktopWidget().screenGeometry()
         self.resize(min(1280, res.width() - 10), min(720, res.height() - 10))
         self.setWindowTitle(self.builder_name)
-        window_icon = resource_filename("pypsbuilder", app_icons[self.builder_name])
+        window_icon = str(
+            ires.files("pypsbuilder").joinpath(app_icons[self.builder_name])
+        )
         self.setWindowIcon(QtGui.QIcon(window_icon))
         self.__changed = False
         self.about_dialog = AboutDialog(self.builder_name, __version__, __copyright__)
@@ -5097,7 +5100,7 @@ class TopologyGraph(QtWidgets.QDialog):
     def __init__(self, ps, parent=None):
         super(TopologyGraph, self).__init__(parent)
         self.setWindowTitle("Topology graph")
-        window_icon = resource_filename("pypsbuilder", "images/pypsbuilder.png")
+        window_icon = str(ires.files("pypsbuilder").joinpath("images/pypsbuilder.png"))
         self.setWindowIcon(QtGui.QIcon(window_icon))
         self.setWindowFlags(
             QtCore.Qt.WindowMinMaxButtonsHint | QtCore.Qt.WindowCloseButtonHint

{pypsbuilder-2.4.2 → pypsbuilder-2.5.1}/pypsbuilder/psclasses.py

@@ -4,6 +4,7 @@ This module contains classes and tools providing API to THERMOCALC, parsing of
 outputs and storage of calculated invariant points and univariant lines.
 
 """
+
 # author: Ondrej Lexa
 # website: https://github.com/ondrolexa/pypsbuilder
 
@@ -473,9 +474,11 @@ class TCResult:
         phases = head.split()[1:]
         # fixed width parsing !!!
         valsf = [
-            float(vals[6:][12 * i : 12 * (i + 1)].strip())
-            if vals[6:][12 * i : 12 * (i + 1)].strip() != ""
-            else 0.0
+            (
+                float(vals[6:][12 * i : 12 * (i + 1)].strip())
+                if vals[6:][12 * i : 12 * (i + 1)].strip() != ""
+                else 0.0
+            )
             for i in range(len(phases))
         ]
         for phase, val in zip(phases, valsf):
@@ -484,9 +487,11 @@ class TCResult:
         head, vals = factor.split("\n")
         phases = head.split()[1:]
         valsf = [
-            float(vals[6:][12 * i : 12 * (i + 1)].strip())
-            if vals[6:][12 * i : 12 * (i + 1)].strip() != ""
-            else 0.0
+            (
+                float(vals[6:][12 * i : 12 * (i + 1)].strip())
+                if vals[6:][12 * i : 12 * (i + 1)].strip() != ""
+                else 0.0
+            )
             for i in range(len(phases))
         ]
         for phase, val in zip(phases, valsf):
@@ -934,6 +939,13 @@ class SectionBase:
                 phases = self.unilines[unilist[0]].phases.difference(
                     self.unilines[unilist[0]].out
                 )
+                if frozenset(phases) in shapes:  # switch polymorph
+                    for pp in polymorphs:
+                        if self.unilines[unilist[0]].out.issubset(pp):
+                            phases = self.unilines[unilist[0]].phases.difference(
+                                pp.difference(self.unilines[unilist[0]].out)
+                            )
+                            break
                 shapes[frozenset(phases)] = poly
                 unilists[frozenset(phases)] = unilist
             elif frozenset(phases) in shapes:

{pypsbuilder-2.4.2 → pypsbuilder-2.5.1}/pypsbuilder/psexplorer.py

@@ -17,6 +17,7 @@ Example:
     >>> pt.show()
 
 """
+
 # author: Ondrej Lexa 2020
 # website: https://github.com/ondrolexa/pypsbuilder
 
@@ -636,12 +637,13 @@ class PS:
         mn, mx = sys.float_info.max, -sys.float_info.max
         recs = OrderedDict()
         for key in self:
-            d = self.collect_data(key, phase, expr, which=which)
-            z = d["data"]
-            if z:
-                recs[key] = d
-                mn = min(mn, min(z))
-                mx = max(mx, max(z))
+            if phase.split("(")[0] in key:
+                d = self.collect_data(key, phase, expr, which=which)
+                z = d["data"]
+                if z:
+                    recs[key] = d
+                    mn = min(mn, min(z))
+                    mx = max(mx, max(z))
             # res = self.grid.gridcalcs[self.grid.masks[key]]
             # if len(res) > 0:
             #     if phase in res[0]['data']:
@@ -948,7 +950,7 @@ class PS:
                 cgd = {}
                 mn, mx = sys.float_info.max, -sys.float_info.max
                 for ix, grid in self.grids.items():
-                    gd = np.empty(grid.xg.shape)
+                    gd = np.empty(grid.xg.shape, dtype=float)
                     gd[:] = np.nan
                     for key in grid.masks:
                         results = grid.gridcalcs[grid.masks[key] & (grid.status == 1)]
@@ -989,9 +991,12 @@ class PS:
         self,
         *args,
         interpolation=None,
+        colors=None,
         label=False,
         skiplabels=0,
         labelfs=6,
+        logerr=True,
+        maxerr=10,
         geterror=False,
         getpt=False,
         fig=None,
@@ -1001,6 +1006,8 @@ class PS:
         smooth=0,
         alpha=0.5,
         lw=2,
+        filename=None,
+        save_kw={},
     ):
         """Function to plot root squared error of calculated and estimated values.
 
@@ -1013,6 +1020,7 @@ class PS:
             interpolation (str): matplotlib imshow interpolation method.
                 Default None.
             label (bool): Whether to label divariant fields. Default False.
+            logerr (bool): When True, plot logarithms of error. Default True
             geterror (bool): When True, calculated RMSE array is returned. Otherwise
                 error is plotted. Deafult False
             getpt (bool): When True return tuple of (p, T, err) where error is minimal.
@@ -1022,6 +1030,8 @@ class PS:
             fig (Figure): If not None, axes are added to fig and returned.
                 Default None
             fig_kw: dict passed to subplots method.
+            filename: If not None, figure is saved to file
+            save_kw: dict passed to savefig method.
             isopleths (bool): When True, searched isopleths are shown. Default False
             which (int): Bitopt defining from where data are collected. 0 bit -
                 invariant points, 1 bit - uniariant lines and 2 bit - GridData
@@ -1038,7 +1048,8 @@ class PS:
         if len(args) % 3 == 0:
             if self.gridded:
                 err = []
-                prop_cycle = plt.rcParams["axes.prop_cycle"]
+                if colors is None:
+                    colors = list(mcolors.TABLEAU_COLORS.keys())[: len(args) // 3]
                 for phase, expr, val in zip(args[::3], args[1::3], args[2::3]):
                     if self.check_phase_expr(phase, expr):
                         err.append(
@@ -1052,6 +1063,7 @@ class PS:
                         )
 
                 err = np.sqrt(sum(err)) / len(err)
+                err[err > maxerr] = np.nan
                 r, c = np.unravel_index(np.nanargmin(err), err.shape)
                 p = self.yspace[r]
                 T = self.xspace[c]
@@ -1073,13 +1085,16 @@ class PS:
                         origin="lower",
                         alpha=alpha,
                     )
-                    ax.contour(self.xspace, self.yspace, err, colors="w")
+                    if logerr:
+                        ax.contour(self.xspace, self.yspace, np.log(err), colors="w")
+                    else:
+                        ax.contour(self.xspace, self.yspace, err, colors="w")
                     if isopleths:
                         for phase, expr, val, cc in zip(
                             args[::3],
                             args[1::3],
                             args[2::3],
-                            prop_cycle.by_key()["color"],
+                            colors,
                         ):
                             if self.check_phase_expr(phase, expr):
                                 ax = self.isopleths_vector(
@@ -1093,9 +1108,14 @@ class PS:
                     ax.set_ylim(self.yrange)
                     fig.colorbar(im)
 
-                    ax.set_title(f"RMSE - MinErr={minerr:g} at {T} {p}")
+                    ax.set_title(f"RMSE - MinErr={minerr:g} at {T:g} {p:g}")
                     fig.tight_layout()
-                    plt.show()
+
+                    if filename is not None:
+                        plt.savefig(filename, **save_kw)
+                        plt.close(fig)
+                    else:
+                        plt.show()
             else:
                 print("Not yet gridded...")
         else:
@@ -1762,10 +1782,10 @@ class PS:
 
         Example:
             >>> pt.overlap_isopleths(
-                    'g', 'xMgX', (0.07, 0.13),
                     'g', 'xFeX', (0.51, 0.65),
-                    'g', 'xCaX', (0.06, 0.15),
+                    'g', 'xMgX', (0.07, 0.13),
                     'g', 'xMnX', (0.16, 0.27),
+                    'g', 'xCaX', (0.06, 0.15),
                 )
         """
         if len(args) % 3 == 0:
@@ -1779,10 +1799,7 @@ class PS:
                 show = kwargs.get("show", None)
                 colors = kwargs.get("colors", None)
                 if colors is None:
-                    cc = list(mcolors.TABLEAU_COLORS.keys())
-                    cixs = np.random.choice(
-                        range(len(cc)), size=len(args) // 3, replace=False
-                    )
+                    colors = list(mcolors.TABLEAU_COLORS.keys())[: len(args) // 3]
                 handles = []
                 if fig is None:
                     if ax is None:
@@ -1796,7 +1813,7 @@ class PS:
                         show = False
                     ax = fig.add_subplot()
                 for phase, expr, levels, color in zip(
-                    args[::3], args[1::3], args[2::3], cixs
+                    args[::3], args[1::3], args[2::3], colors
                 ):
                     ax = self.isopleths(
                         phase,
@@ -1804,20 +1821,19 @@ class PS:
                         levels=levels,
                         colorbar=False,
                         filled_over=True,
-                        colors=[cc[color]],
+                        colors=[color],
                         alpha=alpha,
                         show=False,
                         ax=ax,
                     )
-                    handles.append(
-                        mpatches.Patch(color=cc[color], alpha=alpha, label=expr)
-                    )
+                    handles.append(mpatches.Patch(color=color, alpha=alpha, label=expr))
                 self.add_overlay(ax)
                 ax.legend(handles=handles)
                 # coords
                 ax.format_coord = self.format_coord
                 # connect button press
                 # cid = fig.canvas.mpl_connect('button_press_event', self.onclick)
+                ax.set_title(self.name)
                 if filename is not None:
                     plt.savefig(filename, **save_kw)
                     plt.close(fig)
@@ -2381,7 +2397,7 @@ class PS:
                     self.common_grid_and_masks()
                 #  interpolate on common grid
                 recs, mn, mx = self.merge_data(phase, expr, which=which)
-                gd = np.empty(self.xg.shape)
+                gd = np.empty(self.xg.shape, dtype=float)
                 gd[:] = np.nan
                 for key in recs:
                     xmin, ymin, xmax, ymax = self.shapes[key].bounds