Release of v3.1.1 #patch

Author: ma-sadeghi

.github/workflows/bump-version-dev.yml

@@ -7,19 +7,18 @@ on:
 
 jobs:
   build:
+    if: (! contains(github.event.head_commit.message, '[no bump]'))
+
     name: Bump version
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-        persist-credentials: false  # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
-        fetch-depth: 0              # otherwise, you will failed to push refs to dest repo
+    - uses: actions/checkout@v3
 
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - name: Set env variables
       run: |
@@ -41,14 +40,20 @@ jobs:
         bump_version build $VERSION_FILE
         # Note that we don't want to create a new tag for "builds"
 
-    - name: Commit files
-      run: |
-        REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
-        remote_repo="https://${GITHUB_ACTOR}:${{ secrets.PUSH_ACTION_TOKEN }}@github.com/${REPOSITORY}.git"
+    # - name: Commit files
+    #   run: |
+    #     REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
+    #     remote_repo="https://${GITHUB_ACTOR}:${{ secrets.PUSH_ACTION_TOKEN }}@github.com/${REPOSITORY}.git"
 
-        git config --local user.email "action@github.com"
-        git config --local user.name "GitHub Action"
+    #     git config --local user.email "action@github.com"
+    #     git config --local user.name "GitHub Action"
 
-        # Commit version bump to dev ([no ci] to avoid infinite loop)
-        git commit -m "Bump version number [no ci]" -a
-        git push "${remote_repo}" dev
+    #     # Commit version bump to dev ([no ci] to avoid infinite loop)
+    #     git commit -m "Bump version number (build) [no ci]" -a
+    #     git push "${remote_repo}" dev
+
+    - name: Commit files
+      uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: Bump version number (build part)
+        commit_author: Author <actions@github.com>

openpnm/algorithms/_reactive_transport.py

@@ -1,21 +1,22 @@
-import sys
 import logging
+import sys
+
 import numpy as np
 from numpy.linalg import norm
 from scipy.optimize.nonlin import TerminationCondition
-from openpnm.algorithms import Transport
-from openpnm.utils import TypedList, Docorator
 from tqdm.auto import tqdm
 
+from openpnm.algorithms import Transport
+from openpnm.utils import Docorator, TypedList
 
-__all__ = ['ReactiveTransport']
+__all__ = ["ReactiveTransport"]
 
 
 docstr = Docorator()
 logger = logging.getLogger(__name__)
 
 
-@docstr.get_sections(base='ReactiveTransportSettings', sections=['Parameters'])
+@docstr.get_sections(base="ReactiveTransportSettings", sections=["Parameters"])
 @docstr.dedent
 class ReactiveTransportSettings:
     r"""
@@ -45,7 +46,7 @@ class ReactiveTransportSettings:
     x_rtol = 1e-6
 
 
-@docstr.get_sections(base='ReactiveTransport', sections=['Parameters'])
+@docstr.get_sections(base="ReactiveTransport", sections=["Parameters"])
 @docstr.dedent
 class ReactiveTransport(Transport):
     r"""
@@ -62,11 +63,11 @@ class ReactiveTransport(Transport):
 
     """
 
-    def __init__(self, name='react_trans_?', **kwargs):
+    def __init__(self, name="react_trans_?", **kwargs):
         super().__init__(name=name, **kwargs)
         self.settings._update(ReactiveTransportSettings())
 
-    def set_source(self, pores, propname, mode='add'):
+    def set_source(self, pores, propname, mode="add"):
         r"""
         Applies a given source term to the specified pores
 
@@ -105,21 +106,21 @@ def set_source(self, pores, propname, mode='add'):
         propname = self._parse_prop(propname, "pore")
         # Check if any BC is already set in the same locations
         locs_BC = np.zeros(self.Np, dtype=bool)
-        for item in self['pore.bc'].keys():
-            locs_BC = np.isfinite(self[f'pore.bc.{item}'])
+        for item in self["pore.bc"].keys():
+            locs_BC = np.isfinite(self[f"pore.bc.{item}"])
         if np.any(locs_BC[pores]):
             raise Exception("BCs present in given pores, can't assign source term")
-        prop = 'pore.source.' + propname.split('.', 1)[1]
-        if mode == 'add':
+        prop = "pore.source." + propname.split(".", 1)[1]
+        if mode == "add":
             if prop not in self.keys():
                 self[prop] = False
             self[prop][pores] = True
-        elif mode == 'remove':
+        elif mode == "remove":
             self[prop][pores] = False
-        elif mode == 'clear':
+        elif mode == "clear":
             self[prop] = False
         else:
-            raise Exception(f'Unsupported mode {mode}')
+            raise Exception(f"Unsupported mode {mode}")
 
     def _apply_sources(self):
         """
@@ -134,9 +135,9 @@ def _apply_sources(self):
         """
         try:
             phase = self.project[self.settings.phase]
-            for item in self['pore.source'].keys():
+            for item in self["pore.source"].keys():
                 # Fetch linearized values of the source term
-                Ps = self['pore.source.' + item]
+                Ps = self["pore.source." + item]
                 S1, S2 = [phase[f"pore.{item}.{Si}"] for Si in ["S1", "S2"]]
                 # Modify A and b: diag(A) += -S1, b += S2
                 diag = self.A.diagonal()
@@ -173,20 +174,22 @@ def _run_special(self, solver, x0, verbose=None):
             Initial guess of the unknown variable
 
         """
-        w = self.settings['relaxation_factor']
-        maxiter = self.settings['newton_maxiter']
-        f_rtol = self.settings['f_rtol']
-        x_rtol = self.settings['x_rtol']
+        w = self.settings["relaxation_factor"]
+        maxiter = self.settings["newton_maxiter"]
+        f_rtol = self.settings["f_rtol"]
+        x_rtol = self.settings["x_rtol"]
         xold = self.x
         dx = self.x - xold
-        condition = TerminationCondition(f_tol=np.inf, f_rtol=f_rtol, x_rtol=x_rtol, norm=norm)
+        condition = TerminationCondition(
+            f_tol=np.inf, f_rtol=f_rtol, x_rtol=x_rtol, norm=norm
+        )
 
         tqdm_settings = {
             "total": 100,
             "desc": f"{self.name} : Newton iterations",
             "disable": not verbose,
             "file": sys.stdout,
-            "leave": False
+            "leave": False,
         }
 
         with tqdm(**tqdm_settings) as pbar:
@@ -198,12 +201,12 @@ def _run_special(self, solver, x0, verbose=None):
                 if is_converged:
                     pbar.update(100 - pbar.n)
                     self.soln.is_converged = is_converged
-                    logger.info(f'Solution converged, residual norm: {norm(res):.4e}')
+                    logger.info(f"Solution converged, residual norm: {norm(res):.4e}")
                     return
                 super()._run_special(solver=solver, x0=xold, w=w)
                 dx = self.x - xold
                 xold = self.x
-                logger.info(f'Iteration #{i:<4d} | Residual norm: {norm(res):.4e}')
+                logger.info(f"Iteration #{i:<4d} | Residual norm: {norm(res):.4e}")
                 self.soln.num_iter = i + 1
 
         self.soln.is_converged = False
@@ -217,7 +220,7 @@ def _get_progress(self, res):
             self._f0_norm = norm(res)
         f_rtol = self.settings.f_rtol
         norm_reduction = norm(res) / self._f0_norm / f_rtol
-        progress = (1 - max(np.log10(norm_reduction), 0) / np.log10(1/f_rtol)) * 100
+        progress = (1 - max(np.log10(norm_reduction), 0) / np.log10(1 / f_rtol)) * 100
         return max(0, progress)
 
     def _update_A_and_b(self):
@@ -240,12 +243,12 @@ def _get_residual(self, x=None):
             x = self.x
         return self.A * x - self.b
 
-    def set_BC(self, pores=None, bctype=[], bcvalues=[], mode='add'):
+    def set_BC(self, pores=None, bctype=[], bcvalues=[], mode="add"):
         msg = "Source term already present in given pores, can't assign BCs"
         # Ensure that given pores do not have source terms already set
         try:
-            for item in self['pore.source'].keys():
-                if np.any(self['pore.source.'+item][pores]):
+            for item in self["pore.source"].keys():
+                if np.any(self["pore.source." + item][pores]):
                     raise Exception(msg)
         except KeyError:
             pass