Merge branch 'master' of github.com:oscarbranson/latools

.github/workflows/tests.yml

@@ -10,14 +10,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [windows-latest, ubuntu-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Setup python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

CHANGELOG.md

@@ -1,11 +1,38 @@
 # Changelog
 All significant changes to the software will be documented here.
 
-## [0.3.27-dev] - LIVE
+## [0.3.30-dev] - LIVE
 
 ### TODO
 - implement different analyte lists for different stages (raw, ratios, mass_fractions), OR improve analyte_checker functionality. This has to propagate throught to filter assignment.
 
+## [0.3.30] - 12/01/2024
+
+### Changed
+ - Changed `sklearn` to `scikit-learn` in requirements.txt to accommodate change in upstream package name
+ - Moved from setup.py to setup.cfg for package metadata
+ - Changed version labelling from `__version__` to `VERSION` to match pypi expectations.
+
+
+## [0.3.29]
+
+More pandas 2.0 'indexing with set' compatibility updates...
+
+### Changed
+ - modify dataframe indexing in filt_obj to work with pandas>=2.0.0
+
+
+
+## [0.3.28]
+
+### Changed
+ - minor updates to work with pandas>=2.0.0
+ - plotting updates to use `.get_subplotspec()` when checking row/col status.
+ - minor revisions to GitHub Actions scripts
+
+
+## [0.3.27] missed... oops!
+
 ## [0.3.26]
 
 ### Changed

Supplement/comparison_tools/plots.py

@@ -135,13 +135,13 @@ def comparison_plots(df, els=['Mg', 'Sr', 'Ba', 'Al', 'Mn']):
             ax.plot(xlim, xlim, c='k', ls='dashed', alpha=0.6)
 
         for ax in axs[i]:
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 hax.set_xlabel('Residual')
                 tax.set_xlabel('Reference User')
                 lax.set_xlabel('Reference User')
                 hax.legend(fontsize=8)
 
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 tax.set_title('Manual Test User', loc='left')
                 lax.set_title('LAtools Test User', loc='left')
 
@@ -232,15 +232,15 @@ def residual_plots(df, rep_stats=None, els=['Mg', 'Sr', 'Ba', 'Al', 'Mn']):
             if rep_stats is not None:
                 ax.axhspan(-rep_stats[e][0] * 2, rep_stats[e][0] * 2, color=(0,0,0,0.2), zorder=-1)
 
-            if not ax.is_first_col():
+            if not ax.get_subplotspec().is_first_col():
                 ax.set_yticklabels([])
 
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 hax.set_xlabel('Density')
                 tax.set_xlabel('Reference User')
                 lax.set_xlabel('Reference User')
 
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 tax.set_title('Manual Test User', loc='left')
                 lax.set_title('LAtools Test User', loc='left')
 
@@ -374,21 +374,21 @@ def bland_altman_plots(df, rep_stats=None, els=['Mg', 'Sr', 'Ba', 'Al', 'Mn']):
         for ax in axs[i]:
             ax.set_ylim(ylim)
 
-            if ax.is_first_col():
+            if ax.get_subplotspec().is_first_col():
                 ax.set_ylabel(e + ' ('+ u + ')\nResidual')
             else:
                 ax.set_ylabel('')
                 ax.set_yticklabels([])
 
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 tax.set_xlabel('Mean')
                 lax.set_xlabel('Mean')
                 hax.set_xlabel('Residual Density')
                 hax.legend()
             else:
                 ax.set_xlabel('')
 
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 tax.set_title('Manual Test User', loc='left')
                 lax.set_title('LAtools Test User', loc='left')
                 hax.set_title('Residuals', loc='left')

Supplement/comparison_tools/plots_1sample.py

@@ -81,12 +81,12 @@ def comparison_plots(df, els=['Mg', 'Sr', 'Al', 'Mn', 'Fe', 'Cu', 'Zn', 'B']):
         lax.plot(xlim, xlim, c='k', ls='dashed', alpha=0.6)
 
         for ax in axs[i]:
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 hax.set_xlabel('Residual')
                 lax.set_xlabel('Iolite User')
                 hax.legend(fontsize=8)
 
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 lax.set_title('LAtools', loc='left')
 
     fig.tight_layout()
@@ -164,14 +164,14 @@ def residual_plots(df, rep_stats=None, els=['Mg', 'Sr', 'Al', 'Mn', 'Fe', 'Cu',
             if rep_stats is not None:
                 ax.axhspan(-rep_stats[e][0] * 2, rep_stats[e][0] * 2, color=(0,0,0,0.2), zorder=-1)
 
-            if not ax.is_first_col():
+            if not ax.get_subplotspec().is_first_col():
                 ax.set_yticklabels([])
 
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 hax.set_xlabel('Density')
                 lax.set_xlabel('Iolite User')
 
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 lax.set_title('LAtools', loc='left')
 
     fig.tight_layout()

docs/source/conf.py

@@ -77,9 +77,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = latools.__version__
+version = latools.VERSION
 # The full version, including alpha/beta/rc tags.
-release = latools.__version__
+release = latools.VERSION
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

latools/D_obj.py

@@ -1550,13 +1550,13 @@ def crossplot(self, analytes=None, bins=25, lognorm=True, filt=True, colourful=T
             ax.xaxis.set_visible(False)
             ax.yaxis.set_visible(False)
 
-            if ax.is_first_col():
+            if ax.get_subplotspec().is_first_col():
                 ax.yaxis.set_ticks_position('left')
-            if ax.is_last_col():
+            if ax.get_subplotspec().is_last_col():
                 ax.yaxis.set_ticks_position('right')
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 ax.xaxis.set_ticks_position('top')
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 ax.xaxis.set_ticks_position('bottom')
 
         # set up colour scales
@@ -1664,13 +1664,13 @@ def crossplot_filters(self, filter_string, analytes=None):
             ax.xaxis.set_visible(False)
             ax.yaxis.set_visible(False)
 
-            if ax.is_first_col():
+            if ax.get_subplotspec().is_first_col():
                 ax.yaxis.set_ticks_position('left')
-            if ax.is_last_col():
+            if ax.get_subplotspec().is_last_col():
                 ax.yaxis.set_ticks_position('right')
-            if ax.is_first_row():
+            if ax.get_subplotspec().is_first_row():
                 ax.xaxis.set_ticks_position('top')
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 ax.xaxis.set_ticks_position('bottom')
 
         # isolate nominal_values for all analytes

latools/__init__.py

@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.26'
+VERSION = '0.3.30'
 
 def cite(output='text'):
     """

latools/filtering/filt_obj.py

@@ -117,7 +117,7 @@ def check_analytes(self, analytes=None, single=False, allow_multiples=False):
                 return analytes[0]
             return valid.pop()
         else:
-            return valid
+            return list(valid)
 
     def add(self, name, filt, info='', params=(), setn=None):
         """
@@ -286,9 +286,9 @@ def make_analyte(self, analyte):
             boolean filter
         """
         analyte = self.check_analytes(analyte)
-            
+
         key = []
-        for n, f in self.filter_table[analyte].index[self.filter_table[analyte].any(1)]:
+        for n, f in self.filter_table[analyte].index[self.filter_table[analyte].any(axis=1)]:
             key.append(f'{n}:{f}')
 
         return self.make_fromkey('&'.join(key))

latools/helpers/plot.py

@@ -322,13 +322,13 @@ def crossplot(dat, keys=None, lognorm=True, bins=25, figsize=(12, 12),
         ax.xaxis.set_visible(False)
         ax.yaxis.set_visible(False)
 
-        if ax.is_first_col():
+        if ax.get_subplotspec().is_first_col():
             ax.yaxis.set_ticks_position('left')
-        if ax.is_last_col():
+        if ax.get_subplotspec().is_last_col():
             ax.yaxis.set_ticks_position('right')
-        if ax.is_first_row():
+        if ax.get_subplotspec().is_first_row():
             ax.xaxis.set_ticks_position('top')
-        if ax.is_last_row():
+        if ax.get_subplotspec().is_last_row():
             ax.xaxis.set_ticks_position('bottom')
 
     # set up colour scales
@@ -473,7 +473,7 @@ def histograms(dat, keys=None, bins=25, logy=False, cmap=None, ncol=4):
 
         ax.set_ylim(1, ax.get_ylim()[1])
 
-        if ax.is_first_col():
+        if ax.get_subplotspec().is_first_col():
             ax.set_ylabel(ylab)
 
         ax.set_yticklabels([])
@@ -701,11 +701,11 @@ def autorange_plot(t, sig, gwin=7, swin=None, win=30,
                 ax.text(.95, .95, '{} (off)'.format(n), ha='right',
                         va='top', transform=ax.transAxes)
 
-            if ax.is_last_row():
+            if ax.get_subplotspec().is_last_row():
                 ax.set_xlabel('Time (s)')
-            if ax.is_first_col():
+            if ax.get_subplotspec().is_first_col():
                 ax.set_ylabel('Gradient (x)')
-            if ax.is_last_col():
+            if ax.get_subplotspec().is_last_col():
                 tax.set_ylabel('Signal (line)')
 
             if fail: