pypsbuilder 2.4.1__tar.gz → 2.5.0__tar.gz

{pypsbuilder-2.4.1 → pypsbuilder-2.5.0}/CHANGELOG.md

@@ -1,7 +1,13 @@
 # Changelog
 All notable pypsbuilder changes.
 
-## master
+## [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
@@ -58,7 +64,7 @@ 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-2.4.1 → pypsbuilder-2.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypsbuilder
-Version: 2.4.1
+Version: 2.5.0
 Summary: THERMOCALC front-end for constructing and analyzing PT pseudosections
 Home-page: https://github.com/ondrolexa/pypsbuilder
 Author: Ondrej Lexa
@@ -13,7 +13,7 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Utilities
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.md
@@ -88,7 +88,13 @@ pypsbuilder is free software: you can redistribute it and/or modify it under the
 # Changelog
 All notable pypsbuilder changes.
 
-## master
+## [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
@@ -145,7 +151,7 @@ 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-2.4.1 → pypsbuilder-2.5.0}/docs/conf.py

@@ -75,9 +75,9 @@ author = "Ondrej Lexa"
 # built documents.
 #
 # The short X.Y version.
-version = "2.4"
+version = "2.5"
 # The full version, including alpha/beta/rc tags.
-release = "2.4.1"
+release = "2.5.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pypsbuilder-2.5.0/pyproject.toml

@@ -0,0 +1,50 @@
+[tool.poetry]
+name = "pypsbuilder"
+version = "2.5.0"
+description = "THERMOCALC front-end for constructing and analyzing PT pseudosections"
+authors = ["Ondrej Lexa <lexa.ondrej@gmail.com>"]
+readme = "README.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.test.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-2.4.1 → pypsbuilder-2.5.0}/pypsbuilder/__init__.py

@@ -22,7 +22,7 @@ __all__ = (
     "get_tcapi",
 )
 
-__version__ = "2.4.1"
+__version__ = "2.5.0"
 __author__ = "Ondrej Lexa"
-__copyright__ = "© Ondrej Lexa 2024"
+__copyright__ = "© Ondrej Lexa 2016-2024"
 __email__ = "lexa.ondrej@gmail.com"

{pypsbuilder-2.4.1 → pypsbuilder-2.5.0}/pypsbuilder/psbuilders.py

@@ -14,7 +14,7 @@ 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 +94,7 @@ 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 +5097,7 @@ 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-2.4.1 → pypsbuilder-2.5.0}/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
 
@@ -282,8 +283,8 @@ class UniLine(PseudoBase):
             return candidate
 
         # Check for polymorphs
-        fixi, fixu = False, False
         for poly in polymorphs:
+            fixi, fixu = False, False
             if (
                 poly.issubset(ip.phases)
                 and (poly != ip.out)
@@ -292,20 +293,21 @@ class UniLine(PseudoBase):
                 fixi = True
                 if poly.issubset(self.phases) and not self.out.isdisjoint(poly):
                     fixu = True
+            # check invs
+            candidate = checkme(self.phases, self.out, ip.phases, ip.out)
+            if fixi and not candidate:
+                candidate = checkme(
+                    self.phases,
+                    self.out,
+                    ip.phases,
+                    ip.out.difference(poly).union(poly.difference(ip.out)),
+                )
+            if fixu and not candidate:
+                candidate = checkme(
+                    self.phases, poly.difference(self.out), ip.phases, ip.out
+                )
+            if candidate:
                 break
-        # check invs
-        candidate = checkme(self.phases, self.out, ip.phases, ip.out)
-        if fixi and not candidate:
-            candidate = checkme(
-                self.phases,
-                self.out,
-                ip.phases,
-                ip.out.difference(poly).union(poly.difference(ip.out)),
-            )
-        if fixu and not candidate:
-            candidate = checkme(
-                self.phases, poly.difference(self.out), ip.phases, ip.out
-            )
         return candidate
 
     def get_label_point(self):
@@ -472,9 +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):
@@ -483,9 +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):
@@ -933,6 +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-2.4.1 → pypsbuilder-2.5.0}/pypsbuilder/psexplorer.py

@@ -636,12 +636,13 @@ 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 +949,7 @@ 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 +990,12 @@ class PS:
         self,
         *args,
         interpolation=None,
+        colors=None,
         label=False,
         skiplabels=0,
         labelfs=6,
+        logerr=True,
+        maxerr=10,
         geterror=False,
         getpt=False,
         fig=None,
@@ -999,6 +1003,10 @@ class PS:
         isopleths=False,
         which=7,
         smooth=0,
+        alpha=0.5,
+        lw=2,
+        filename=None,
+        save_kw={},
     ):
         """Function to plot root squared error of calculated and estimated values.
 
@@ -1011,6 +1019,7 @@ 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.
@@ -1020,7 +1029,9 @@ class PS:
             fig (Figure): If not None, axes are added to fig and returned.
                 Default None
             fig_kw: dict passed to subplots method.
-            isopleths (bool): When True, searched isoplots are shown.Default False
+            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
                 points
@@ -1036,6 +1047,8 @@ class PS:
         if len(args) % 3 == 0:
             if self.gridded:
                 err = []
+                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(
@@ -1049,6 +1062,7 @@ 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]
@@ -1068,13 +1082,22 @@ class PS:
                         interpolation=interpolation,
                         aspect="auto",
                         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 in zip(args[::3], args[1::3], args[2::3]):
+                        for phase, expr, val, cc in zip(
+                            args[::3],
+                            args[1::3],
+                            args[2::3],
+                            colors,
+                        ):
                             if self.check_phase_expr(phase, expr):
                                 ax = self.isopleths_vector(
-                                    phase, expr, levels=[val], ax=ax
+                                    phase, expr, levels=[val], ax=ax, lw=lw, color=cc
                                 )
                     ax.plot(T, p, "r*", ms=20)
                     self.add_overlay(
@@ -1084,9 +1107,14 @@ 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:
@@ -1714,10 +1742,10 @@ class PS:
                     table(ax=ax, cellText=[val1, val2], colLabels=ox, loc="top")
             else:
                 if only is None:
-                    if show is None or show is True:
-                        ax.set_xlim(self.xrange)
-                        ax.set_ylim(self.yrange)
-                        ax.set_title("{}({})".format(phase, expr))
+                    # if show is None or show is True:
+                    ax.set_xlim(self.xrange)
+                    ax.set_ylim(self.yrange)
+                    ax.set_title("{}({})".format(phase, expr))
                 else:
                     ax.set_title("{} - {}({})".format(" ".join(only), phase, expr))
             # coords
@@ -1746,13 +1774,17 @@ 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.
+            show (bool): When False, Axes are returned, otherwise plot is shown.
+                Default True
 
         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:
@@ -1766,10 +1798,7 @@ 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:
@@ -1783,7 +1812,7 @@ 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,
@@ -1791,20 +1820,19 @@ 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)
@@ -1858,16 +1886,17 @@ class PS:
             overlay (bool): Whether to show assemblage fields. Default True
             high (frozenset or list): Highlight divariant fields identified
                 by key(s).
-            cmap (str): matplotlib colormap used to divariant fields coloring.
-                Colors are based on variance. Default 'viridis'.
+            cmap (str): matplotlib colormap used isopleths coloring. Default 'viridis'.
             bulk (bool): Whether to show bulk composition on top of diagram.
                 Default False.
             fig (Figure): If not None, axes are added to fig and returned.
                 Default None
             fig_kw: dict passed to subplots method.
+            lw (float): Linewidth of isopleths. Default 1.0
             ax (Axes): Axes to be used. Default None
             filename: If not None, figure is saved to file
             save_kw: dict passed to savefig method.
+            color: matplotlib color for isopleths. If None cmap is used. Default None.
             show (bool): When False, Axes are returned, otherwise plot is shown.
                 Default True
         """
@@ -1893,9 +1922,11 @@ class PS:
             method = kwargs.get("method", "rbf")
             rbf_func = kwargs.get("rbf_func", "thin_plate")
             cmap = kwargs.get("cmap", "viridis")
+            color = kwargs.get("color", None)
             colorbar = kwargs.get("colorbar", True)
             fig = kwargs.get("fig", None)
             fig_kw = kwargs.get("fig_kw", {})
+            lw = kwargs.get("lw", 1.0)
             ax = kwargs.get("ax", None)
             filename = kwargs.get("filename", None)
             save_kw = kwargs.get("save_kw", {})
@@ -2085,11 +2116,19 @@ class PS:
                                     for lnp in ln.geoms:
                                         lnp = lnp.simplify(tolerance=0.01)
                                         x, y = np.array(lnp.coords).T
-                                        ax.plot(x, y, color=mapper.to_rgba(v))
+                                        if color is None:
+                                            ax.plot(
+                                                x, y, color=mapper.to_rgba(v), lw=lw
+                                            )
+                                        else:
+                                            ax.plot(x, y, color=color, lw=lw)
                                 else:
                                     ln = ln.simplify(tolerance=0.01)
                                     x, y = np.array(ln.coords).T
-                                    ax.plot(x, y, color=mapper.to_rgba(v))
+                                    if color is None:
+                                        ax.plot(x, y, color=mapper.to_rgba(v), lw=lw)
+                                    else:
+                                        ax.plot(x, y, color=color, lw=lw)
             if only is None:
                 if overlay:
                     self.add_overlay(ax)
@@ -2357,7 +2396,7 @@ 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

{pypsbuilder-2.4.1 → pypsbuilder-2.5.0}/pypsbuilder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pypsbuilder
-Version: 2.4.1
+Version: 2.5.0
 Summary: THERMOCALC front-end for constructing and analyzing PT pseudosections
 Home-page: https://github.com/ondrolexa/pypsbuilder
 Author: Ondrej Lexa
@@ -13,7 +13,7 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Utilities
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.md
@@ -88,7 +88,13 @@ pypsbuilder is free software: you can redistribute it and/or modify it under the
 # Changelog
 All notable pypsbuilder changes.
 
-## master
+## [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
@@ -145,7 +151,7 @@ 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-2.4.1 → pypsbuilder-2.5.0}/pypsbuilder.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ CONTRIBUTING.md
 LICENSE
 MANIFEST.in
 README.md
+pyproject.toml
 setup.cfg
 setup.py
 docs/Makefile

{pypsbuilder-2.4.1 → pypsbuilder-2.5.0}/setup.cfg

@@ -1,11 +1,13 @@
 [bumpversion]
-current_version = 2.4.1
+current_version = 2.5.0
 commit = True
 tag = True
 tag_name = {new_version}
 
 [bumpversion:file:setup.py]
 
+[bumpversion:file:pyproject.toml]
+
 [bumpversion:file:docs/conf.py]
 
 [bumpversion:file:pypsbuilder/__init__.py]

{pypsbuilder-2.4.1 → pypsbuilder-2.5.0}/setup.py

@@ -15,7 +15,7 @@ requirements = ["numpy", "matplotlib>=3", "scipy", "networkx", "shapely>=2", "tq
 
 setup(
     name="pypsbuilder",
-    version="2.4.1",
+    version="2.5.0",
     description="THERMOCALC front-end for constructing and analyzing PT pseudosections",
     long_description=readme + "\n\n" + changelog,
     long_description_content_type="text/markdown",
@@ -23,7 +23,7 @@ setup(
     author_email="lexa.ondrej@gmail.com",
     url="https://github.com/ondrolexa/pypsbuilder",
     license="MIT",
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     packages=find_packages(),
     package_data={"pypsbuilder.images": ["*.png"]},
     entry_points="""