WIP: PEP 503/625 compatibility and Windows MPI tests

.github/workflows/beta-master.yml

@@ -13,8 +13,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-13, ubuntu-latest, windows-latest] # TODO: Unpin mac version when cvxopt or Python 3.8 dropped
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: [3.9, '3.10', '3.11', '3.12']
         use-cython: ['true', 'false']
     uses: ./.github/workflows/reuseable-main.yml
     name: Run pyGSTi tests

.github/workflows/develop.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest] # No Mac
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11', '3.12']
         use-cython: ['true', 'false']
     uses: ./.github/workflows/reuseable-main.yml
     name: Run pyGSTi tests

.github/workflows/feature-branches.yml

@@ -18,17 +18,17 @@ jobs:
     strategy:
       # fail-fast: true is OK here
       matrix:
-        os: [ubuntu-latest, windows-latest] # No Mac
-        python-version: [3.8, '3.11'] # Only extremal Python versions
+        os: [macos-latest, ubuntu-latest, windows-latest] # TEMP: Try latest mac again # No Mac
+        python-version: [3.9, '3.12'] # Only extremal Python versions
     uses: ./.github/workflows/reuseable-main.yml
     name: Run pyGSTi tests
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
       use-cython: 'true' # Only test environment with Cython
       run-unit-tests: 'true'
-      run-extra-tests: 'false' # No integration tests
-      run-notebook-tests: 'false' # No notebook tests 
+      run-extra-tests: 'true' # No integration tests # TEMP: Try integration tests
+      run-notebook-tests: 'true' # No notebook tests # TEMP: Try notebook tests
 
 
 

.github/workflows/reuseable-main.yml

@@ -34,14 +34,19 @@ jobs:
     runs-on: ${{ inputs.os }}
     steps:
     - uses: actions/checkout@v4
-    - name: Set up installation environment (Linux and Windows)
-      if: ${{ inputs.os != 'macos-13' }}
+    - name: Set up installation environment (Linux)
+      if: ${{ inputs.os == 'ubuntu-latest' }}
       run: |
         ./.github/ci-scripts/before_install.sh
     - name: Set up installation environment (MacOS)
-      if: ${{ inputs.os == 'macos-13' }}
+      if: ${{ inputs.os == 'macos-latest' }}
       run: |
         ./.github/ci-scripts/before_install_macos.sh
+    - name: Set up MPI (Windows)
+      if: ${{ inputs.os == 'windows-latest' }}
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: intelmpi
     - name: Set up Python ${{ inputs.python-version }}
       uses: actions/setup-python@v5
       with:

README.md

@@ -36,7 +36,7 @@ In particular, there are a number of characterization protocols currently implem
 
 PyGSTi is designed with a modular structure so as to be highly customizable
 and easily integrated to new or existing python software.  It runs using
-python 3.8 or higher.  To faclilitate integration with software for running
+python 3.9 or higher.  To faclilitate integration with software for running
 cloud-QIP experiments, pyGSTi `Circuit` objects can be converted to IBM's
 **OpenQASM** and Rigetti Quantum Computing's **Quil** circuit description languages.
 

pygsti/baseobjs/label.py

@@ -128,13 +128,13 @@ def __new__(cls, name, state_space_labels=None, time=None, args=None):
 
         #print(" -> preproc with name=", name, "sslbls=", state_space_labels, "t=", time, "args=", args)
         if state_space_labels is None or state_space_labels in ((), (None,)):
-            if args:
+            if args is not None:
                 return LabelTupWithArgs.init(name, (), time, args)  # just use empty sslbls
             else:
                 return LabelStr.init(name, time)
 
         else:
-            if args: return LabelTupWithArgs.init(name, state_space_labels, time, args)
+            if args is not None: return LabelTupWithArgs.init(name, state_space_labels, time, args)
             else:
                 if time == 0.0:
                     return LabelTup.init(name, state_space_labels)

pygsti/evotypes/chp/povmreps.py

@@ -51,7 +51,7 @@ def _run_chp_ops(self, chp_ops):
 
         # Extract outputs
         #print("CHP program out (debug): ", out.decode('utf-8'))
-        pattern = _re.compile('Outcome of measuring qubit (\d+): (\d)( ?\S*)')
+        pattern = _re.compile(r'Outcome of measuring qubit (\d+): (\d)( ?\S*)')
         matched_values = []  # elements = (qubit_index, outcome, '(random)' or '') tuples
         for match in pattern.finditer(out.decode('utf-8')):
             matched_values.append((int(match.group(1)), match.group(2), match.group(3)))

pygsti/report/formatters.py

@@ -67,7 +67,7 @@ def _no_format(x, specs):
                         ebstring='%s <span class="errorbar">&plusmn; %s</span>',
                         nmebstring='%s <span class="nmerrorbar">&plusmn; %s</span>')
 NormalLatex = _Formatter(latex,
-                         ebstring='$ \\begin{array}{c} %s \\\\ \pm %s \\end{array} $')  # nmebstring will match
+                         ebstring='$ \\begin{array}{c} %s \\\\ \\pm %s \\end{array} $')  # nmebstring will match
 
 # Normal replacements
 format_dict['Normal'] = {
@@ -186,7 +186,7 @@ def special_convert_latex(x, specs):
 
 format_dict['Vec'] = {
     'html': NormalHTML,
-    'latex': _Formatter(latex, ebstring='%s $\pm$ %s'),
+    'latex': _Formatter(latex, ebstring='%s $\\pm$ %s'),
     'python': _no_format}
 
 format_dict['Circuit'] = {

pygsti/report/html.py

@@ -149,10 +149,10 @@ def vector(v, specs):
         lines.append(value(el, specs, mathmode=True))
     if specs['brackets']:
         return "$ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} $\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} $\n"
     else:
         return "$ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} $\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} $\n"
 
 
 def matrix(m, specs):
@@ -177,18 +177,18 @@ def matrix(m, specs):
     fontsize = specs['fontsize']
 
     if fontsize is not None:
-        prefix += "\\fontsize{%f}{%f}\selectfont " % (fontsize, fontsize * 1.2)
+        prefix += "\\fontsize{%f}{%f}\\selectfont " % (fontsize, fontsize * 1.2)
 
     for r in range(m.shape[0]):
         lines.append(" & ".join(
             [value(el, specs, mathmode=True) for el in m[r, :]]))
 
     if specs['brackets']:
         return prefix + "$ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} $\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} $\n"
     else:
         return prefix + "$ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} $\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} $\n"
 
 
 def value(el, specs, mathmode=False):

pygsti/report/latex.py

@@ -50,9 +50,9 @@ def table(custom_headings, col_headings_formatted, rows, spec):
             and "latex" in custom_headings:
         latex = custom_headings['latex']
     else:
-        latex = "\\begin{%s}[l]{%s}\n\hline\n" % \
+        latex = "\\begin{%s}[l]{%s}\n\\hline\n" % \
             (table, "|c" * len(col_headings_formatted) + "|")
-        latex += ("%s \\\\ \hline\n"
+        latex += ("%s \\\\ \\hline\n"
                   % (" & ".join(col_headings_formatted)))
 
     for formatted_rowData in rows:
@@ -82,9 +82,9 @@ def table(custom_headings, col_headings_formatted, rows, spec):
             #        latex += "\cline{%d-%d} "%(lineStart,col-1)
             #    latex += "\n"
             #else:
-            latex += " \\\\ \hline\n"
+            latex += " \\\\ \\hline\n"
 
-    latex += "\end{%s}\n" % table
+    latex += "\\end{%s}\n" % table
     return {'latex': latex}
 
 
@@ -129,7 +129,7 @@ def list(l, specs):
         latex string for l.
     """
     return "\\begin{tabular}{c}\n" + \
-        " \\\\ \n".join(l) + "\n \end{tabular}\n"
+        " \\\\ \n".join(l) + "\n \\end{tabular}\n"
 
 
 def vector(v, specs):
@@ -154,10 +154,10 @@ def vector(v, specs):
         lines.append(value(el, specs, mathmode=True))
     if specs['brackets']:
         return "\\ensuremath{ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} }\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} }\n"
     else:
         return "\\ensuremath{ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} }\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} }\n"
 
 
 def matrix(m, specs):
@@ -182,18 +182,18 @@ def matrix(m, specs):
     fontsize = specs['fontsize']
 
     if fontsize is not None:
-        prefix += "\\fontsize{%f}{%f}\selectfont " % (fontsize, fontsize * 1.2)
+        prefix += "\\fontsize{%f}{%f}\\selectfont " % (fontsize, fontsize * 1.2)
 
     for r in range(m.shape[0]):
         lines.append(" & ".join(
             [value(el, specs, mathmode=True) for el in m[r, :]]))
 
     if specs['brackets']:
         return prefix + "\\ensuremath{ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} }\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} }\n"
     else:
         return prefix + "\\ensuremath{ \\begin{pmatrix}\n" + \
-            " \\\\ \n".join(lines) + "\n \end{pmatrix} }\n"
+            " \\\\ \n".join(lines) + "\n \\end{pmatrix} }\n"
 
 
 def value(el, specs, mathmode=False):
@@ -304,5 +304,5 @@ def escaped(txt, specs):
     -------
     string
     """
-    ret = txt.replace("_", "\_")
+    ret = txt.replace("_", r"\_")
     return ret

pygsti/report/reportables.py

@@ -15,7 +15,7 @@
  used primarily in reports, so we refer to these quantities as
  "reportables".
 """
-import pkgutil
+import importlib
 import warnings as _warnings
 
 import numpy as _np
@@ -32,7 +32,7 @@
 from pygsti.models.explicitmodel import ExplicitOpModel as _ExplicitOpModel
 
 
-_CVXPY_AVAILABLE = pkgutil.find_loader('cvxpy') is not None
+_CVXPY_AVAILABLE = importlib.util.find_spec('cvxpy') is not None
 
 FINITE_DIFF_EPS = 1e-7
 

pygsti/report/workspacetables.py

@@ -2213,10 +2213,10 @@ def _create(self, model, confidence_region_info, show_axis_angle_err_bars):
         formatters = [None] * nCols
 
         table = "tabular"
-        latex_head = "\\begin{%s}[l]{%s}\n\hline\n" % (table, "|c" * nCols + "|")
+        latex_head = "\\begin{%s}[l]{%s}\n\\hline\n" % (table, "|c" * nCols + "|")
         latex_head += "\\multirow{2}{*}{Gate} & \\multirow{2}{*}{Angle} & " + \
-                      "\\multicolumn{%d}{c|}{Angle between Rotation Axes} \\\\ \cline{3-%d}\n" % (len(opLabels), nCols)
-        latex_head += " & & %s \\\\ \hline\n" % (" & ".join(map(str, opLabels)))
+                      "\\multicolumn{%d}{c|}{Angle between Rotation Axes} \\\\ \\cline{3-%d}\n" % (len(opLabels), nCols)
+        latex_head += " & & %s \\\\ \\hline\n" % (" & ".join(map(str, opLabels)))
 
         table = _ReportTable(colHeadings, formatters,
                              custom_header={'latex': latex_head}, confidence_region_info=confidence_region_info)
@@ -2834,8 +2834,8 @@ def _create(self, xs, circuits_by_x, model_by_x, dataset, objfn_builder, x_label
         if objfn_builder == "chi2" or (isinstance(objfn_builder, _objfns.ObjectiveFunctionBuilder)
                                        and objfn_builder.cls_to_build == _objfns.Chi2Function):
             colHeadings = {
-                'latex': (x_label, '$\\chi^2$', '$k$', '$\\chi^2-k$', '$\sqrt{2k}$',
-                          '$N_\\sigma$', '$N_s$', '$N_p$', 'Rating'),
+                'latex': (x_label, r'$\chi^2$', '$k$', r'$\chi^2-k$', r'$\sqrt{2k}$',
+                          r'$N_\sigma$', '$N_s$', '$N_p$', 'Rating'),
                 'html': (x_label, '&chi;<sup>2</sup>', 'k', '&chi;<sup>2</sup>-k',
                          '&radic;<span style="text-decoration:overline;">2k</span>',
                          'N<sub>sigma</sub>', 'N<sub>s</sub>', 'N<sub>p</sub>', 'Rating'),
@@ -2845,8 +2845,8 @@ def _create(self, xs, circuits_by_x, model_by_x, dataset, objfn_builder, x_label
         elif objfn_builder == "logl" or (isinstance(objfn_builder, _objfns.ObjectiveFunctionBuilder)
                                          and objfn_builder.cls_to_build == _objfns.PoissonPicDeltaLogLFunction):
             colHeadings = {
-                'latex': (x_label, '$2\Delta\\log(\\mathcal{L})$', '$k$', '$2\Delta\\log(\\mathcal{L})-k$',
-                          '$\sqrt{2k}$', '$N_\\sigma$', '$N_s$', '$N_p$', 'Rating'),
+                'latex': (x_label, r'$2\Delta\log(\mathcal{L})$', '$k$', r'$2\Delta\log(\mathcal{L})-k$',
+                          r'$\sqrt{2k}$', r'$N_\sigma$', '$N_s$', '$N_p$', 'Rating'),
                 'html': (x_label, '2&Delta;(log L)', 'k', '2&Delta;(log L)-k',
                          '&radic;<span style="text-decoration:overline;">2k</span>',
                          'N<sub>sigma</sub>', 'N<sub>s</sub>', 'N<sub>p</sub>', 'Rating'),
@@ -2948,9 +2948,9 @@ def _create(self, circuit_lists, titles, num_cols, common_title):
         else:
             table = "tabular"
             colHeadings = ('\\#',) + tuple(titles)
-            latex_head = "\\begin{%s}[l]{%s}\n\hline\n" % (table, "|c" * len(colHeadings) + "|")
-            latex_head += " & \multicolumn{%d}{c|}{%s} \\\\ \hline\n" % (len(colHeadings) - 1, common_title)
-            latex_head += "%s \\\\ \hline\n" % (" & ".join(colHeadings))
+            latex_head = "\\begin{%s}[l]{%s}\n\\hline\n" % (table, "|c" * len(colHeadings) + "|")
+            latex_head += " & \\multicolumn{%d}{c|}{%s} \\\\ \\hline\n" % (len(colHeadings) - 1, common_title)
+            latex_head += "%s \\\\ \\hline\n" % (" & ".join(colHeadings))
 
             colHeadings = ('#',) + tuple(titles)
             html_head = '<table class="%(tableclass)s" id="%(tableid)s" ><thead>'
@@ -3149,9 +3149,9 @@ def _create(self, metric, models, target_models, titles,
         #html_head += "</thead><tbody>"
 
         if table_title:
-            latex_head = "\\begin{tabular}[l]{%s}\n\hline\n" % ("|c" * nCols + "|")
-            latex_head += "\\multicolumn{%d}{c|}{%s} \\\\ \cline{1-%d}\n" % (nCols, table_title, nCols)
-            latex_head += " & ".join(colHeadings) + "\\\\ \hline\n"
+            latex_head = "\\begin{tabular}[l]{%s}\n\\hline\n" % ("|c" * nCols + "|")
+            latex_head += "\\multicolumn{%d}{c|}{%s} \\\\ \\cline{1-%d}\n" % (nCols, table_title, nCols)
+            latex_head += " & ".join(colHeadings) + "\\\\ \\hline\n"
 
             html_head = '<table class="%(tableclass)s" id="%(tableid)s" ><thead>'
             html_head += '<tr><th colspan="%d">%s</th></tr>\n' % (nCols, table_title)
@@ -3406,8 +3406,8 @@ def _create(self, model, params_dict):
         formatters = ('Bold', 'Bold')
 
         #custom latex header for maximum width imposed on 2nd col
-        latex_head = "\\begin{tabular}[l]{|c|p{3in}|}\n\hline\n"
-        latex_head += "\\textbf{Quantity} & \\textbf{Value} \\\\ \hline\n"
+        latex_head = "\\begin{tabular}[l]{|c|p{3in}|}\n\\hline\n"
+        latex_head += "\\textbf{Quantity} & \\textbf{Value} \\\\ \\hline\n"
         table = _ReportTable(colHeadings, formatters,
                              custom_header={'latex': latex_head})
 
@@ -3513,8 +3513,8 @@ def _get_package_version(module_name):
         formatters = ('Bold', 'Bold')
 
         #custom latex header for maximum width imposed on 2nd col
-        latex_head = "\\begin{tabular}[l]{|c|p{3in}|}\n\hline\n"
-        latex_head += "\\textbf{Quantity} & \\textbf{Value} \\\\ \hline\n"
+        latex_head = "\\begin{tabular}[l]{|c|p{3in}|}\n\\hline\n"
+        latex_head += "\\textbf{Quantity} & \\textbf{Value} \\\\ \\hline\n"
         table = _ReportTable(colHeadings, formatters,
                              custom_header={'latex': latex_head})
 
@@ -3583,8 +3583,8 @@ def _create(self, profiler, sort_by):
         formatters = ('Bold', 'Bold')
 
         #custom latex header for maximum width imposed on 2nd col
-        latex_head = "\\begin{tabular}[l]{|c|p{3in}|}\n\hline\n"
-        latex_head += "\\textbf{Label} & \\textbf{Time} (sec) \\\\ \hline\n"
+        latex_head = "\\begin{tabular}[l]{|c|p{3in}|}\n\\hline\n"
+        latex_head += "\\textbf{Label} & \\textbf{Time} (sec) \\\\ \\hline\n"
         table = _ReportTable(colHeadings, formatters,
                              custom_header={'latex': latex_head})
 

pygsti/tools/optools.py

@@ -753,7 +753,7 @@ def unitarity(a, mx_basis="gm"):
     noise" NJP 17 113020 (2015). The unitarity is given by (Prop 1 in Wallman
     et al):
 
-    `u(a) = Tr( A_u^{\dagger} A_u ) / (d^2  - 1)`,
+    `u(a) = Tr( A_u^{\\dagger} A_u ) / (d^2  - 1)`,
 
     where A_u is the unital submatrix of a, and d is the dimension of
     the Hilbert space. When a is written in any basis for which the

setup.py

@@ -131,7 +131,7 @@ def build_extensions(self):
 
 def setup_with_extensions(extensions=None):
     setup(
-        name='pyGSTi',
+        name='pygsti',
         use_scm_version=custom_version,
         cmdclass={'build_ext': build_ext_compiler_check},
         description='A python implementation of Gate Set Tomography',
@@ -277,10 +277,10 @@ def setup_with_extensions(extensions=None):
             'networkx'
         ],
         extras_require=extras,
-        python_requires='>=3.8',
+        python_requires='>=3.9',
         platforms=["any"],
         url='http://www.pygsti.info',
-        download_url='https://github.com/pyGSTio/pyGSTi/tarball/master',
+        download_url='https://github.com/sandialabs/pyGSTi/tarball/master',
         keywords=[
             'pygsti',
             'tomography',

test/test_packages/extras/test_interpygate.py

@@ -12,7 +12,7 @@
     _comm = MPI.COMM_WORLD
     _rank = _comm.Get_rank()
     _size = _comm.Get_size()
-except (ImportError, RuntimeError):
+except ImportError: # Reverted RuntimeError to cause Windows runners to break
     _comm = None
     _rank = 0
     _size = 1