Merge branch 'release/0.23.0.1' into release_update

# Conflicts:
#	recipe.yaml

Author: domfournier

.github/workflows/issue_to_jira.yml

@@ -4,10 +4,17 @@ on:
   issues:
     types: [opened]
 
+permissions:
+  contents: read
+  issues: write
+
 jobs:
   call-workflow-create-jira-issue:
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@main
-    secrets: inherit
     with:
       project-key: 'GEOPY'
       components: '[{"name": "simpeg"}]'
+    secrets:
+      JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
+      JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
+      JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}

.github/workflows/pr_add_jira_summary.yml

@@ -1,10 +1,16 @@
 name: Add JIRA issue summary
 
 on:
-  pull_request_target:
+  pull_request_target:  # zizmor: ignore[dangerous-triggers]
     types: [opened]
 
+permissions:
+  contents: read
+  pull-requests: write
+
 jobs:
   call-workflow-add-jira-issue-summary:
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-pr_add_jira_summary.yml@main
-    secrets: inherit
+    secrets:
+      JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
+      JIRA_BASIC_AUTH: ${{ secrets.JIRA_BASIC_AUTH }}

.github/workflows/pull_request.yml

@@ -68,7 +68,7 @@ jobs:
           persist-credentials: false
 
       - name: flake8 review
-        uses: reviewdog/action-flake8@v3
+        uses: reviewdog/action-flake8@b65981e158319f08cb7d0132f28bc0081e110adc # v3.15.2
         with:
           workdir: pr_source
           github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -104,7 +104,7 @@ jobs:
           path: 'pr_source'
           persist-credentials: false
 
-      - uses: reviewdog/action-black@v3
+      - uses: reviewdog/action-black@644053a260402bc4278a865906107bd8aef7fae8 # v3.22.4
         with:
           workdir: 'pr_source'
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python_deploy_dev.yml

@@ -13,6 +13,9 @@ jobs:
   call-workflow-conda-publish:
     name: Publish development conda package on JFrog Artifactory
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_rattler_package.yml@main
+    permissions:
+      contents: write  # to create draft release and attach artifacts
+      actions: read
     with:
       package-name: 'mira-simpeg'
       python-version: '3.10'
@@ -25,6 +28,9 @@ jobs:
   call-workflow-pypi-publish:
     name: Publish development pypi package (JFrog Artifactory, TestPyPI)
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main
+    permissions:
+      contents: write  # to create draft release and attach artifacts
+      actions: read
     with:
       package-manager: 'setuptools'
       package-name: 'mira-simpeg'

.github/workflows/python_deploy_prod.yml

@@ -28,8 +28,11 @@ jobs:
     name: Publish production Conda package on JFrog Artifactory
     if: ${{ github.event_name == 'release' || github.event.inputs.publish-conda == 'true' }}
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_conda_assets.yml@main
+    permissions:
+      contents: write  # seems required to find the draft release
+      actions: read
     with:
-      virtual-repo-names: '["public-conda-prod"]'
+      virtual-repo-names: '["public-noremote-conda-prod"]'
       release-tag: ${{ github.event.release.tag_name || github.event.inputs.release-tag }}
     secrets:
       JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }}
@@ -38,6 +41,9 @@ jobs:
     name: Publish production PyPI package (JFrog Artifactory, PyPI)
     if: ${{ github.event_name == 'release' || github.event.inputs.publish-pypi == 'true' }}
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_pypi_assets.yml@main
+    permissions:
+      contents: write  # seems required to find the draft release
+      actions: read
     with:
       package-name: 'mira-simpeg'
       virtual-repo-names: '["public-pypi-prod", "pypi"]'

pyproject.toml

@@ -35,6 +35,7 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Mathematics",
     "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX",
     "Operating System :: Unix",

simpeg/dask/electromagnetics/time_domain/simulation.py

@@ -11,6 +11,7 @@
 from dask import array, delayed
 from dask.distributed import get_client
 
+from time import time
 from simpeg.dask.utils import get_parallel_blocks
 from simpeg.utils import mkvc
 
@@ -405,10 +406,6 @@ def get_field_deriv_block(
         # Cut out early data
         time_check = np.kron(time_mask, np.ones(shape, dtype=bool))[rx_ind]
         local_ind = np.arange(rx_ind.shape[0])[time_check]
-
-        if len(local_ind) < 1:
-            continue
-
         indices.append(
             (np.arange(count, count + len(local_ind)), local_ind),
         )
@@ -425,14 +422,14 @@ def get_field_deriv_block(
 
         stacked_blocks.append(stacked_block)
 
-    if len(stacked_blocks) > 0:
-        blocks = np.hstack(stacked_blocks)
-
+    blocks = np.hstack(stacked_blocks)
+    if blocks.ndim == 2 and blocks.shape[1] > 0:
         solve = (AdiagTinv * blocks).reshape(blocks.shape)
     else:
         solve = None
 
     updated_ATinv_df_duT_v = []
+
     for (_, arrays), field_deriv, ATinv_chunk, (columns, local_ind) in zip(
         block, field_derivs, ATinv_df_duT_v, indices, strict=True
     ):
@@ -444,10 +441,9 @@ def get_field_deriv_block(
             )
             ATinv_chunk = np.zeros(shape, dtype=np.float32)
 
-        if solve is None:
-            continue
+        if solve is not None:
+            ATinv_chunk[:, local_ind] = solve[:, columns]
 
-        ATinv_chunk[:, local_ind] = solve[:, columns]
         updated_ATinv_df_duT_v.append(ATinv_chunk)
 
     return updated_ATinv_df_duT_v

simpeg/dask/objective_function.py

@@ -15,6 +15,10 @@ def _calc_dpred(objfct, _):
     return objfct.simulation.dpred(m=objfct.simulation.model)
 
 
+def _calc_objective(objfct, multiplier, model):
+    return multiplier * objfct(model)
+
+
 def _calc_residual(objfct, _):
     return objfct.W * (
         objfct.data.dobs - objfct.simulation.dpred(m=objfct.simulation.model)
@@ -33,6 +37,18 @@ def _store_model(objfct, model):
     objfct.simulation.model = model
 
 
+def _setter_broadcast(objfct, key, value):
+    """
+    Broadcast a value to all workers.
+    """
+    if hasattr(objfct, key):
+        setattr(objfct, key, value)
+
+    for sim in objfct.simulation.simulations:
+        if hasattr(sim, key):
+            setattr(sim, key, value)
+
+
 def _get_jtj_diag(objfct, _):
     jtj = objfct.simulation.getJtJdiag(objfct.simulation.model, objfct.W)
     return jtj.flatten()
@@ -56,14 +72,15 @@ def _validate_type_or_future_of_type(
         property_name, objects, obj_type, ensure_unique=True
     )
     workload = [[]]
+    lookup = {}
     count = 0
     for obj in objects:
         if count == len(workers):
             count = 0
             workload.append([])
         obj.simulation.simulations[0].worker = workers[count]
         future = client.scatter([obj], workers=workers[count])[0]
-
+        lookup[obj] = (future, workers[count])
         if hasattr(obj, "name"):
             future.name = obj.name
 
@@ -84,7 +101,7 @@ def _validate_type_or_future_of_type(
         raise TypeError(f"{property_name} futures must be an instance of {obj_type}")
 
     if return_workers:
-        return workload, workers
+        return workload, workers, lookup
     else:
         return workload
 
@@ -374,7 +391,7 @@ def objfcts(self):
     def objfcts(self, objfcts):
         client = self.client
 
-        futures, workers = _validate_type_or_future_of_type(
+        futures, workers, lookup = _validate_type_or_future_of_type(
             "objfcts",
             objfcts,
             L2DataMisfit,
@@ -387,6 +404,11 @@ def objfcts(self, objfcts):
         self._futures = futures
         self._workers = workers
 
+        self._lookup = {
+            misfit.simulation: (future, worker)
+            for misfit, (future, worker) in lookup.items()
+        }
+
     def residuals(self, m, f=None):
         """
         Compute the residual for the data misfit.
@@ -411,3 +433,26 @@ def residuals(self, m, f=None):
             residuals += client.gather(future_residuals)
 
         return residuals
+
+    def broadcast_updates(self, updates: dict):
+        """
+        Set the attributes of the objective functions and simulations
+        """
+        stores = []
+        client = self.client
+        for fun, (key, value) in updates.items():
+            if fun not in self._lookup:
+                continue
+
+            future, worker = self._lookup[fun]
+
+            stores.append(
+                client.submit(
+                    _setter_broadcast,
+                    future,
+                    key,
+                    value,
+                    workers=worker,
+                )
+            )
+        self.client.gather(stores)  # blocking call to ensure all models were stored

simpeg/directives/_regularization.py

@@ -229,19 +229,20 @@ def adjust_cooling_schedule(self):
         """
         Adjust the cooling schedule based on the misfit.
         """
-        ratio = self.invProb.phi_d / self.misfit_from_chi_factor(self.chifact_target)
+        if self.metrics.start_irls_iter is None:
+            return
 
-        if (
-            np.abs(1.0 - ratio) > self.misfit_tolerance
-            and self.metrics.start_irls_iter is not None
-        ):
+        ratio = self.invProb.phi_d / self.misfit_from_chi_factor(self.chifact_target)
+        if np.abs(1.0 - ratio) > self.misfit_tolerance:
 
             if ratio > 1:
-                ratio = np.mean([2.0, ratio])
+                update_ratio = 1 / np.mean([0.75, 1 / ratio])
             else:
-                ratio = np.mean([0.75, ratio])
+                update_ratio = 1 / np.mean([2.0, 1 / ratio])
 
-            self.cooling_factor = ratio
+            self.cooling_factor = update_ratio
+        else:
+            self.cooling_factor = 1.0
 
     def initialize(self):
         """

simpeg/directives/_save_geoh5.py

@@ -379,9 +379,7 @@ def write(self, iteration: int, **_):
         with open(dirpath / "SimPEG.log", "r", encoding="utf-8") as file:
             iteration = 0
             for line in file:
-                val = re.findall(
-                    "[+\-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)", line  # noqa
-                )
+                val = re.findall(r"[+-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+-]?\d+)", line)
                 if len(val) == 5:
                     log.append(val[:-2])
                     iteration += 1