From 81db2106b08b970810aff65b444b3365187775d7 Mon Sep 17 00:00:00 2001
From: Oscar Branson <oscarbranson@gmail.com>
Date: Mon, 12 Sep 2022 09:22:22 +0100
Subject: [PATCH 01/18] dev version bump

---
 latools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/latools/__init__.py b/latools/__init__.py
index 347791e..201d076 100644
--- a/latools/__init__.py
+++ b/latools/__init__.py
@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.26'
+__version__ = '0.3.27-dev'
 
 def cite(output='text'):
     """

From f9e97ade356dbbeb41972a5c048633218ce6da9c Mon Sep 17 00:00:00 2001
From: Oscar Branson <oscarbranson@gmail.com>
Date: Fri, 18 Nov 2022 10:14:56 +0000
Subject: [PATCH 02/18] fix issue with analyte being set

---
 latools/latools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/latools/latools.py b/latools/latools.py
index 19c774d..69b60c0 100644
--- a/latools/latools.py
+++ b/latools/latools.py
@@ -4030,13 +4030,13 @@ def getstats(self, filename=None, samples=None, subset=None, ablation_time=False
                     nms = np.array([nm] * reps.size)
                     # make sub - dataframe
                     stdf = pd.DataFrame(self.stats[nm][s].T,
-                                        columns=self.stats[nm]['analytes'],
+                                        columns=list(self.stats[nm]['analytes']),
                                         index=[ss, nms, reps])
                     stdf.index.set_names(['statistic', 'sample', 'rep'],
                                          inplace=True)
                 else:
                     stdf = pd.DataFrame(self.stats[nm][s],
-                                        index=self.stats[nm]['analytes'],
+                                        index=list(self.stats[nm]['analytes']),
                                         columns=[[s], [nm]]).T
 
                     stdf.index.set_names(['statistic', 'sample'],

From 02eb7a2ad54022cfa7420a0804c8c62aac435b57 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 24 Mar 2023 16:01:58 +0000
Subject: [PATCH 03/18] update python versions

---
 .github/workflows/tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 3a5bc30..18f0e9a 100644
--- a/.github/workflows/tests.yml
+++ b/.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: ["3.7", "3.8", "3.9"]
         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 }}
 

From ebdc5aaebbe5b31bc4fb5775bbd70d62afff3701 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 24 Mar 2023 17:05:54 +0000
Subject: [PATCH 04/18] updates to address deprecated matplotlib
 is_[first/last]_[row/col]() method

---
 Supplement/comparison_tools/plots.py         | 16 ++++++++--------
 Supplement/comparison_tools/plots_1sample.py | 10 +++++-----
 latools/D_obj.py                             | 16 ++++++++--------
 latools/helpers/plot.py                      | 16 ++++++++--------
 latools/latools.py                           | 10 +++++-----
 5 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/Supplement/comparison_tools/plots.py b/Supplement/comparison_tools/plots.py
index 5f5fffe..1ca0baa 100644
--- a/Supplement/comparison_tools/plots.py
+++ b/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')
             
@@ -374,13 +374,13 @@ 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')
@@ -388,7 +388,7 @@ def bland_altman_plots(df, rep_stats=None, els=['Mg', 'Sr', 'Ba', 'Al', 'Mn']):
             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')
diff --git a/Supplement/comparison_tools/plots_1sample.py b/Supplement/comparison_tools/plots_1sample.py
index 454098b..48e9055 100644
--- a/Supplement/comparison_tools/plots_1sample.py
+++ b/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()
diff --git a/latools/D_obj.py b/latools/D_obj.py
index 774bd56..7879f82 100644
--- a/latools/D_obj.py
+++ b/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
diff --git a/latools/helpers/plot.py b/latools/helpers/plot.py
index cdc6092..01c1dc7 100644
--- a/latools/helpers/plot.py
+++ b/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:
diff --git a/latools/latools.py b/latools/latools.py
index 69b60c0..f520b0c 100644
--- a/latools/latools.py
+++ b/latools/latools.py
@@ -3167,7 +3167,7 @@ def gradient_histogram(self, analytes=None, win=15, filt=False, bins=None, sampl
             ax.axvline(0, ls='dashed', lw=1, c=(0,0,0,0.7))
 
             ax.set_title(a, loc='left')
-            if ax.is_first_col():
+            if ax.get_subplotspec().is_first_col():
                 ax.set_ylabel('N')
             ax.set_xlabel(u + '/s')
 
@@ -3442,13 +3442,13 @@ 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')
 
         cmlist = ['Blues', 'BuGn', 'BuPu', 'GnBu',

From c15bd071fe49789d677c95b636ef5de23ee48c95 Mon Sep 17 00:00:00 2001
From: Oscar Branson <oscarbranson@gmail.com>
Date: Tue, 28 Mar 2023 12:20:18 +0100
Subject: [PATCH 05/18] attempt to fix 'too many open files' warning on mac

---
 latools/latools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/latools/latools.py b/latools/latools.py
index 69b60c0..523540a 100644
--- a/latools/latools.py
+++ b/latools/latools.py
@@ -3586,10 +3586,10 @@ def trace_plots(self, analytes=None, samples=None, ranges=False,
                 #     ax.axvspan(l, u, color='r', alpha=0.1)
                 # for l, u in s.bkgrng:
                 #     ax.axvspan(l, u, color='k', alpha=0.1)
-                f.savefig(os.path.join(outdir, s + '_traces.pdf'))
+                with open(os.path.join(outdir, s + '_traces.pdf')) as file:
+                    f.savefig(file)
                 # TODO: on older(?) computers raises
                 # 'OSError: [Errno 24] Too many open files'
-                plt.close(f)
                 prog.update()
         return
 

From 1acb47b95e22b53c1fc72c59f0919b2f3a410732 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Tue, 12 Sep 2023 17:57:43 +0800
Subject: [PATCH 06/18] tweaks to accommodate pandas>=2.0  - no longer accepts
 sets as indices  - Multi-dimensional indexing (e.g. `obj[:, None]`) is no
 longer supported.

---
 latools/helpers/analytes.py |  2 +-
 latools/latools.py          | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/latools/helpers/analytes.py b/latools/helpers/analytes.py
index 13feeab..b5aeb58 100644
--- a/latools/helpers/analytes.py
+++ b/latools/helpers/analytes.py
@@ -195,7 +195,7 @@ def analyte_checker(self, analytes=None, check_ratios=True, single=False, focus_
             raise ValueError(f'{analytes} matches more than one valid analyte ({out}). Please be more specific.')
         return out.pop()
 
-    return out
+    return list(out)
 
 def split_analyte_ratios(ratios):
     out = set()
diff --git a/latools/latools.py b/latools/latools.py
index f520b0c..4b3fffe 100644
--- a/latools/latools.py
+++ b/latools/latools.py
@@ -990,10 +990,9 @@ def bkg_calc_weightedmean(self, analytes=None, weight_fwhm=600,
             * 'calibrated': ratio data calibrated to standards, created by self.calibrate.
         """
         if analytes is None:
-            analytes = self.analytes
             self.bkg = Bunch()
-        elif isinstance(analytes, str):
-            analytes = [analytes]
+            
+        analytes = self._analyte_checker(analytes=analytes)
 
         self.get_background(n_min=n_min, n_max=n_max,
                             bkg_filter=bkg_filter,
@@ -1014,9 +1013,11 @@ def bkg_calc_weightedmean(self, analytes=None, weight_fwhm=600,
             self.bkg['calc']['uTime'] = bkg_t
 
         # TODO : calculation then dict assignment is clumsy...
-        mean, std, stderr = gauss_weighted_stats(self.bkg['raw'].uTime,
-                                                 self.bkg['raw'].loc[:, analytes].values,
-                                                 self.bkg['calc']['uTime'],
+        print(analytes)
+
+        mean, std, stderr = gauss_weighted_stats(x=self.bkg['raw'].uTime.values,
+                                                 yarray=self.bkg['raw'].loc[:, analytes].values,
+                                                 x_new=self.bkg['calc']['uTime'],
                                                  fwhm=weight_fwhm)
         self.bkg_interps = {}
 
@@ -1073,10 +1074,9 @@ def bkg_calc_interp1d(self, analytes=None, kind=1, n_min=10, n_max=None, cstep=3
             * 'calibrated': ratio data calibrated to standards, created by self.calibrate.            
         """
         if analytes is None:
-            analytes = self.analytes
             self.bkg = Bunch()
-        elif isinstance(analytes, str):
-            analytes = [analytes]
+            
+        analytes = self._analyte_checker(analytes=analytes)
 
         self.get_background(n_min=n_min, n_max=n_max,
                             bkg_filter=bkg_filter,

From 2b5446f8c478b6e0ab49e35e2ed7a3292c6a7e5e Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Tue, 12 Sep 2023 19:02:34 +0800
Subject: [PATCH 07/18] updates to work with pandas>=2.0

---
 latools/filtering/filt_obj.py |  4 ++--
 latools/helpers/analytes.py   |  2 +-
 latools/latools.py            | 24 +++++++++++-------------
 tests/test_beginnersGuide.py  | 10 +++++-----
 4 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/latools/filtering/filt_obj.py b/latools/filtering/filt_obj.py
index 990637a..54e5509 100644
--- a/latools/filtering/filt_obj.py
+++ b/latools/filtering/filt_obj.py
@@ -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[list(analyte)].index[self.filter_table[list(analyte)].any(axis=1)]:
             key.append(f'{n}:{f}')
         
         return self.make_fromkey('&'.join(key))
diff --git a/latools/helpers/analytes.py b/latools/helpers/analytes.py
index b5aeb58..13feeab 100644
--- a/latools/helpers/analytes.py
+++ b/latools/helpers/analytes.py
@@ -195,7 +195,7 @@ def analyte_checker(self, analytes=None, check_ratios=True, single=False, focus_
             raise ValueError(f'{analytes} matches more than one valid analyte ({out}). Please be more specific.')
         return out.pop()
 
-    return list(out)
+    return out
 
 def split_analyte_ratios(ratios):
     out = set()
diff --git a/latools/latools.py b/latools/latools.py
index 7416573..58e278e 100644
--- a/latools/latools.py
+++ b/latools/latools.py
@@ -1013,10 +1013,8 @@ def bkg_calc_weightedmean(self, analytes=None, weight_fwhm=600,
             self.bkg['calc']['uTime'] = bkg_t
 
         # TODO : calculation then dict assignment is clumsy...
-        print(analytes)
-
         mean, std, stderr = gauss_weighted_stats(x=self.bkg['raw'].uTime.values,
-                                                 yarray=self.bkg['raw'].loc[:, analytes].values,
+                                                 yarray=self.bkg['raw'].loc[:, list(analytes)].values,
                                                  x_new=self.bkg['calc']['uTime'],
                                                  fwhm=weight_fwhm)
         self.bkg_interps = {}
@@ -1585,12 +1583,12 @@ def srm_id_auto(self, srms_used=['NIST610', 'NIST612', 'NIST614'], analytes=None
         analytes = list(analytes)
         
         # get and scale mean srm values for all analytes
-        srmid = self.srmtab.loc[:, idx[analytes, 'mean']]   
+        srmid = self.srmtab.loc[:, idx[list(analytes), 'mean']]   
         _srmid = scale(np.log(srmid))
         srm_labels = srmid.index.values
 
         # get and scale measured srm values for all analytes
-        stdid = self.stdtab.loc[:, idx[analytes, 'mean']]
+        stdid = self.stdtab.loc[:, idx[list(analytes), 'mean']]
         _stdid = scale(np.log(stdid))
         _stdid[np.isnan(_stdid)] = -12
 
@@ -1615,7 +1613,7 @@ def srm_build_calib_table(self):
         caltab = self.stdtab.reset_index()
         caltab.set_index(['gTime', 'uTime'], inplace=True)
         levels = ['meas_' + c if c != '' else c for c in caltab.columns.levels[1]]
-        caltab.columns.set_levels(levels, 1, inplace=True)
+        caltab.columns = caltab.columns.set_levels(levels, level=1)
 
         for a in self.analyte_ratios:
             caltab.loc[:, (a, 'srm_mean')] = self.srmtab.loc[caltab.SRM, (a, 'mean')].values
@@ -1685,7 +1683,7 @@ def calibrate(self, analytes=None, drift_correct=True,
         # make container for calibration params
         gTime = np.asanyarray(self.caltab.index.levels[0])
         if not hasattr(self, 'calib_params'):
-            self.calib_params = pd.DataFrame(columns=pd.MultiIndex.from_product([analytes, ['m']]),
+            self.calib_params = pd.DataFrame(columns=pd.MultiIndex.from_product([list(analytes), ['m']]),
                                              index=gTime)
 
         if zero_intercept:
@@ -1757,8 +1755,8 @@ def calibrate(self, analytes=None, drift_correct=True,
         maxuT = np.max([d.uTime.max() for d in self.data.values()])  # calculate max uTime
         self.calib_params.loc[maxuT, :] = self.calib_params.loc[self.calib_params.index.max(), :]
         # sort indices for slice access
-        self.calib_params.sort_index(1, inplace=True)
-        self.calib_params.sort_index(0, inplace=True)
+        self.calib_params.sort_index(axis=1, inplace=True)
+        self.calib_params.sort_index(axis=0, inplace=True)
 
         # calculcate interpolators for applying calibrations
         self.calib_ps = Bunch()
@@ -3399,7 +3397,7 @@ def filter_effect(self, analytes=None, stats=['mean', 'std'], filt=True):
         comp = comp.join(pd.concat(rats, 1))
         comp.sort_index(1, inplace=True)
         
-        return comp.loc[:, (pd.IndexSlice[:], pd.IndexSlice[analytes])]
+        return comp.loc[:, (pd.IndexSlice[:], pd.IndexSlice[list(analytes)])]
 
     def crossplot_filters(self, filter_string, analytes=None,
                           samples=None, subset=None, filt=None):
@@ -3561,7 +3559,7 @@ def trace_plots(self, analytes=None, samples=None, ranges=False,
         if outdir is None:
             outdir = os.path.join(self.report_dir, focus_stage)
         if not os.path.isdir(outdir):
-            os.mkdir(outdir)
+            os.makedirs(outdir)
 
         analytes = self.analytes_sorted(analytes, focus_stage=focus_stage)
 
@@ -3586,7 +3584,7 @@ def trace_plots(self, analytes=None, samples=None, ranges=False,
                 #     ax.axvspan(l, u, color='r', alpha=0.1)
                 # for l, u in s.bkgrng:
                 #     ax.axvspan(l, u, color='k', alpha=0.1)
-                with open(os.path.join(outdir, s + '_traces.pdf')) as file:
+                with open(os.path.join(outdir, s + '_traces.pdf'), 'wb') as file:
                     f.savefig(file)
                 # TODO: on older(?) computers raises
                 # 'OSError: [Errno 24] Too many open files'
@@ -3880,7 +3878,7 @@ def sample_stats(self, analytes=None, filt=True,
 
         with self.pbar.set(total=len(samples), desc='Calculating Stats') as prog:
             for s in samples:
-                self.data[s].sample_stats(analytes, filt=filt,
+                self.data[s].sample_stats(analytes, filt=1616,
                                           stat_fns=stat_fns,
                                           eachtrace=eachtrace,
                                           focus_stage=focus_stage)
diff --git a/tests/test_beginnersGuide.py b/tests/test_beginnersGuide.py
index 1589370..9083057 100644
--- a/tests/test_beginnersGuide.py
+++ b/tests/test_beginnersGuide.py
@@ -8,11 +8,11 @@ class test_docscode(unittest.TestCase):
     print('\n\nTesting Beginners Guide code examples.')
     if not os.path.exists('./latools_demo_tmp'):
         os.mkdir('./latools_demo_tmp')
-    os.chdir('latools_demo_tmp')
+    # os.chdir('latools_demo_tmp')
 
-    la.get_example_data('./latools_demo_tmp')
+    la.get_example_data('./latools_demo_tmp/latools_demo_tmp')
 
-    eg = la.analyse(data_path='./latools_demo_tmp',  # the location of your data
+    eg = la.analyse(data_path='./latools_demo_tmp/latools_demo_tmp',  # the location of your data
                     config='UCD-AGILENT',  # the configuration to use
                     internal_standard='Ca43',  # the internal standard in your analyses
                     srm_identifier='STD')  # the text that identifies which files contain standard reference materials
@@ -62,8 +62,8 @@ class test_docscode(unittest.TestCase):
     # OK To change line numbers after here.
 
     # clean up
-    os.chdir('..')
-    shutil.rmtree('latools_demo_tmp')
+    # os.chdir('..')
+    shutil.rmtree('./latools_demo_tmp/latools_demo_tmp')
 
     print('\nDone.\n\n')
 

From f251ac2b66cb2c264764950b22a13a3bbad31ad4 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Tue, 12 Sep 2023 19:11:11 +0800
Subject: [PATCH 08/18] version bump and changelog

---
 CHANGELOG.md        | 9 ++++++++-
 latools/__init__.py | 2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5585c65..a9b0790 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,18 @@
 # Changelog
 All significant changes to the software will be documented here.
 
-## [0.3.27-dev] - LIVE
+## [0.3.28-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.
 
+## [0.3.27]
+
+### 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
+
 ## [0.3.26]
 
 ### Changed
diff --git a/latools/__init__.py b/latools/__init__.py
index 201d076..d8d7b2c 100644
--- a/latools/__init__.py
+++ b/latools/__init__.py
@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.27-dev'
+__version__ = '0.3.28'
 
 def cite(output='text'):
     """

From 62471f9df1d9ddc62b60134863271442786246fe Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Tue, 12 Sep 2023 19:25:31 +0800
Subject: [PATCH 09/18] fix versioning in CHANGELOG

---
 CHANGELOG.md | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a9b0790..502effd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,18 +1,21 @@
 # Changelog
 All significant changes to the software will be documented here.
 
-## [0.3.28-dev] - LIVE
+## [0.3.29-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.
 
-## [0.3.27]
+## [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
 
+
+## [0.3.28] missed... oops!
+
 ## [0.3.26]
 
 ### Changed

From e2dc38642b9c3ac89e6394a9865eb8a3669103ea Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Wed, 13 Sep 2023 13:18:53 +0800
Subject: [PATCH 10/18] fixed import errors

---
 latools/latools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/latools/latools.py b/latools/latools.py
index 58e278e..6e7d3a8 100644
--- a/latools/latools.py
+++ b/latools/latools.py
@@ -23,6 +23,7 @@
 
 import uncertainties as unc
 import uncertainties.unumpy as un
+from uncertainties.unumpy import nominal_values, std_devs
 
 from sklearn.preprocessing import minmax_scale, scale
 from sklearn.cluster import KMeans
@@ -42,7 +43,7 @@
 from .helpers import logging
 from .helpers.logging import _log
 from .helpers.config import read_configuration, config_locator
-from .helpers.stat_fns import *
+from .helpers.stat_fns import gauss_weighted_stats, R2calc, stderr, un_interp1d, H15_mean, H15_std, H15_se
 from .helpers import utils
 from .helpers import srm as srms
 from .helpers.progressbars import progressbar

From f396234c8ca2408fe9bebc5c6cd481db3a07aaa2 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Wed, 13 Sep 2023 13:19:31 +0800
Subject: [PATCH 11/18] fixed pandas 2.0 indexing with set error

---
 latools/filtering/filt_obj.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/latools/filtering/filt_obj.py b/latools/filtering/filt_obj.py
index 54e5509..72dd945 100644
--- a/latools/filtering/filt_obj.py
+++ b/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):
         """
@@ -288,7 +288,7 @@ def make_analyte(self, analyte):
         analyte = self.check_analytes(analyte)
         
         key = []
-        for n, f in self.filter_table[list(analyte)].index[self.filter_table[list(analyte)].any(axis=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))

From 4a3589cd8e22782178b124f87a7f98eb76903246 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Wed, 13 Sep 2023 13:21:59 +0800
Subject: [PATCH 12/18] version bump

---
 CHANGELOG.md        | 13 +++++++++++--
 latools/__init__.py |  2 +-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 502effd..11c1e38 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,20 @@
 # Changelog
 All significant changes to the software will be documented here.
 
-## [0.3.29-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.
 
+## [0.3.29]
+
+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
@@ -14,7 +23,7 @@ All significant changes to the software will be documented here.
  - minor revisions to GitHub Actions scripts
 
 
-## [0.3.28] missed... oops!
+## [0.3.27] missed... oops!
 
 ## [0.3.26]
 
diff --git a/latools/__init__.py b/latools/__init__.py
index d8d7b2c..efd7cf7 100644
--- a/latools/__init__.py
+++ b/latools/__init__.py
@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.28'
+__version__ = '0.3.29'
 
 def cite(output='text'):
     """

From cb4abc35de69aea0130ff78ae75356284dc098fc Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 12 Jan 2024 07:18:02 +0000
Subject: [PATCH 13/18] move to setup.cfg; remove sklearn requirement

---
 latools/__init__.py |  3 ++-
 setup.cfg           | 29 +++++++++++++++++++++++++++++
 setup.py            | 44 +-------------------------------------------
 3 files changed, 32 insertions(+), 44 deletions(-)
 create mode 100644 setup.cfg

diff --git a/latools/__init__.py b/latools/__init__.py
index efd7cf7..8039d59 100644
--- a/latools/__init__.py
+++ b/latools/__init__.py
@@ -17,7 +17,8 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.29'
+__version__ = '0.3.30-dev'
+VERSION = __version__
 
 def cite(output='text'):
     """
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..b666048
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,29 @@
+[metadata]
+name = latools
+version = attr: latools.VERSION
+author = Oscar Branson
+author_email = ob266@cam.ac.uk
+description = Tools for LA-ICPMS data analysis.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/oscarbranson/latools
+license = MIT
+project_urls =
+    PalaeoCarb Project = https://github.com/PalaeoCarb
+classifiers =
+    Programming Language :: Python :: 3
+    Intended Audience :: Science/Research
+    Topic :: Scientific/Engineering
+    Programming Language :: Python :: 3
+
+[options]
+python_requires = >3.6
+install_requires = 
+    numpy
+    pandas
+    matplotlib
+    uncertainties
+    scikit-learn
+    scipy
+    Ipython
+include_package_data  = True
diff --git a/setup.py b/setup.py
index a732e82..45642b9 100644
--- a/setup.py
+++ b/setup.py
@@ -1,45 +1,3 @@
 from setuptools import setup, find_packages
 
-# bcause TravisCI was being a jerK
-try:
-  from latools import __version__
-except:
-  __version__ = "version_missing"
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-setup(name='latools',
-      version=__version__,
-      description='Tools for LA-ICPMS data analysis.',
-      long_description=long_description,
-      long_description_content_type="text/markdown",
-      url='https://github.com/oscarbranson/latools',
-      author='Oscar Branson',
-      author_email='oscarbranson@gmail.com',
-      license='MIT',
-      packages=find_packages(),
-      classifiers=['Development Status :: 4 - Beta',
-                   'Intended Audience :: Science/Research',
-                   'Topic :: Scientific/Engineering',
-                   'Programming Language :: Python :: 2',
-                   'Programming Language :: Python :: 3',
-                   ],
-      python_requires='>3.6',
-      install_requires=['numpy',
-                        'pandas',
-                        'matplotlib',
-                        'uncertainties',
-                        'sklearn',
-                        'scipy',
-                        'Ipython',
-                        'configparser',
-                        'tqdm'
-                        ],
-      package_data={
-        'latools': ['latools.cfg',
-                    'resources/*',
-                    'resources/data_formats/*',
-                    'resources/test_data/*'],
-      },
-      zip_safe=False)
+setup(packages=find_packages())

From e2197bb650ae952cab4f88bf98252a01dd6d213c Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 12 Jan 2024 07:23:09 +0000
Subject: [PATCH 14/18] moved to VERSION to work with PyPi schema

---
 latools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/latools/__init__.py b/latools/__init__.py
index 8039d59..bee9fbc 100644
--- a/latools/__init__.py
+++ b/latools/__init__.py
@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.30-dev'
+__version__ = '0.3.30'
 VERSION = __version__
 
 def cite(output='text'):

From 5574cb6d1d7fab58980336e567a0aa3fd721e61a Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 12 Jan 2024 07:26:44 +0000
Subject: [PATCH 15/18] move to newer python versions

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 18f0e9a..5c725e4 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [windows-latest, ubuntu-latest, macos-latest]
 
     steps:

From 3471cad1341238f04eed71fe996ba4f4d189460e Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 12 Jan 2024 07:27:47 +0000
Subject: [PATCH 16/18] add setuptools as a requirement

---
 requirements.txt | 3 ++-
 setup.cfg        | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 813cc91..fbeb189 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,4 +6,5 @@ tqdm>=4.14
 matplotlib>=2.1
 scikit-learn>=0.19
 ipython
-tqdm
\ No newline at end of file
+tqdm
+setuptools
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index b666048..d504583 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,4 +26,5 @@ install_requires =
     scikit-learn
     scipy
     Ipython
+    setuptools
 include_package_data  = True

From 0fb641067be46ca144ad4336fb858e3b51fbd932 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 12 Jan 2024 07:30:40 +0000
Subject: [PATCH 17/18] complete move to VERSION instead of __version__

---
 docs/source/conf.py | 4 ++--
 latools/__init__.py | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 327017b..ab7f075 100644
--- a/docs/source/conf.py
+++ b/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.
diff --git a/latools/__init__.py b/latools/__init__.py
index bee9fbc..b64e39d 100644
--- a/latools/__init__.py
+++ b/latools/__init__.py
@@ -17,8 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.30'
-VERSION = __version__
+VERSION = '0.3.30'
 
 def cite(output='text'):
     """

From a9cd0de93d458d60cdbce3d0dc053108e8e0e8f1 Mon Sep 17 00:00:00 2001
From: Oscar Branson <ob266@cam.ac.uk>
Date: Fri, 12 Jan 2024 07:36:07 +0000
Subject: [PATCH 18/18] 0.3.30 updates

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 11c1e38..9376cc6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,14 @@ All significant changes to the software will be documented here.
 ### 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...