copy setup.py from pyiron_module_template

.binder/environment.yml

@@ -1,15 +1,16 @@
 channels:
-  - conda-forge
+- conda-forge
 dependencies:
-  - damask=3.0.0
-  - matplotlib
-  - fenics
-  - mshr
-  - pyiron_base
-  - pyiron_snippets >=0.1.0,<0.2.0
-  - pyiron-data
-  - pyvista
-  - scipy
-  - seaborn
-  - pip:
-    - git+https://github.com/pyiron/pyiron_continuum.git
+- coveralls
+- atomistics =0.1.32
+- coverage
+- codacy-coverage
+- matplotlib =3.9.2
+- numpy =1.26.4
+- pyiron_base =0.9.12
+- pyiron_snippets =0.1.4
+- scipy =1.14.1
+- sympy =1.13.2
+- python-blosc2
+- python-damask =3.0.0b
+- mendeleev =0.17.0

.binder/postBuild

@@ -0,0 +1,29 @@
+# pip install main
+pip install --no-deps .
+# Note: This produces build and pyiron_continuum.egg-info directories
+
+# clean up
+if [ -d "notebooks" ]; then
+    mv notebooks/* .
+fi
+if [ -d "${HOME}/pyiron_continuum" ]; then
+    rm -r   ${HOME}/.binder \
+            ${HOME}/.ci_support \
+            ${HOME}/.github \
+            ${HOME}/build \
+            ${HOME}/docs \
+            ${HOME}/notebooks \
+            ${HOME}/pyiron_continuum \
+            ${HOME}/pyiron_continuum.egg-info \
+            ${HOME}/tests \
+            ${HOME}/.gitattributes \
+            ${HOME}/.gitignore \
+            ${HOME}/.gitpod \
+            ${HOME}/.readthedocs.yml \
+            ${HOME}/CODE_OF_CONDUCT.md \
+            ${HOME}/CONTRIBUTING.rst \
+            ${HOME}/LICENSE \
+            ${HOME}/MANIFEST.in \
+            ${HOME}/pyproject.toml \
+            ${HOME}/setup.py
+fi

.gitattributes

@@ -0,0 +1 @@
+pyiron_continuum/_version.py export-subst

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a bug report to help us eliminate issues and improve pyiron_continuum
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what the bug is.-->
+
+**pyiron Version and Platform**
+
+<!--Please specify precisely how you installed pyiron and configured pyiron. Post your .pyiron configuration and list your pyiron version.-->
+
+**Expected Behavior**
+
+<!--Describe the expected behavior.-->
+
+**Actual Behavior**
+
+<!--Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.-->
+
+**Steps to Reproduce**
+
+<!--Describe the steps required to (quickly) reproduce the issue.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Make a suggestion for a new feature or a change to pyiron_continuum
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a brief and concise description of the suggested feature or change-->
+
+**Detailed Description**
+
+<!--Please explain how you would like to see pyiron_continuum enhanced, what feature(s) you are looking for, what specific problems this will solve.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/PULL_REQUEST_TEMPLATE/bug_fix.md

@@ -0,0 +1,24 @@
+---
+name: Bug fix
+about: Submit a pull request that fixes one or more bugs
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Briefly describe the bug(s) that are eliminated by this pull request.-->
+
+**Related Issue(s)**
+
+<!--If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged-->
+
+**Backward Compatibility**
+
+<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
+
+**Detailed Description**
+
+<!--Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in pyiron are affected-->

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -0,0 +1,24 @@
+---
+name: New Feature
+about: Submit a pull request that adds new Features (complete files) to pyiron
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Briefly describe the new feature(s) included in this pull request.-->
+
+**Related Issue(s)**
+
+<!--If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged-->
+
+**Backward Compatibility**
+
+<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
+
+**Implementation Notes**
+
+<!--Provide any relevant details about how the new feature(s) are implemented, how correctness was verified, how other features - if any - in pyiron are affected-->

.github/stale.yml

@@ -0,0 +1,58 @@
+# Configuration for probot-stale - https://github.com/probot/stale
+
+# Number of days of inactivity before an Issue or Pull Request becomes stale
+daysUntilStale: 14
+
+# Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
+# Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
+daysUntilClose: 14
+
+# Only issues or pull requests with all of these labels are check if stale. Defaults to `[]` (disabled)
+onlyLabels: []
+
+# Issues or Pull Requests with these labels will never be considered stale. Set to `[]` to disable
+exemptLabels: []
+
+# Set to true to ignore issues in a project (defaults to false)
+exemptProjects: false
+
+# Set to true to ignore issues in a milestone (defaults to false)
+exemptMilestones: false
+
+# Set to true to ignore issues with an assignee (defaults to false)
+exemptAssignees: false
+
+# Label to use when marking as stale
+staleLabel: stale
+
+# Comment to post when marking as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+
+# Comment to post when removing the stale label.
+# unmarkComment: >
+#   Your comment here.
+
+# Comment to post when closing a stale Issue or Pull Request.
+# closeComment: >
+#   Your comment here.
+
+# Limit the number of actions per hour, from 1-30. Default is 30
+limitPerRun: 30
+
+# Limit to only `issues` or `pulls`
+only: pulls
+
+# Optionally, specify configuration settings that are specific to just 'issues' or 'pulls':
+# pulls:
+#   daysUntilStale: 30
+#   markComment: >
+#     This pull request has been automatically marked as stale because it has not had
+#     recent activity. It will be closed if no further activity occurs. Thank you
+#     for your contributions.
+
+# issues:
+#   exemptLabels:
+#     - confirmed

.github/workflows/daily.yml

@@ -0,0 +1,12 @@
+# This runs cron jobs daily
+
+name: Daily
+
+on:
+  schedule:
+    - cron: '0 23 * * *'
+
+jobs:
+  codeql:
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit

.github/workflows/dependabot-pr.yml

@@ -1,10 +1,10 @@
-name: UpdateDependabotPR
-
-on:
-  pull_request_target:
-    branches: [ main ]
-
-jobs:
-  pyiron:
-    uses: pyiron/actions/.github/workflows/[email protected]
-    secrets: inherit
+name: UpdateDependabotPR
+
+on:
+  pull_request_target:
+    branches: [ main ]
+
+jobs:
+  pyiron:
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit

.github/workflows/pr-labeled.yml

@@ -0,0 +1,12 @@
+# This runs jobs which pyiron modules should run when a PR is labeled
+
+name: PR labeled
+
+on:
+  pull_request:
+    types: [labeled]
+
+jobs:
+  pyiron:
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit

.github/workflows/pr-target-opened.yml

@@ -0,0 +1,12 @@
+# This runs jobs which pyiron modules should run when a PR target is opened
+
+name: PR opened
+
+on:
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  pyiron:
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit

.github/workflows/preview-release.yml

@@ -0,0 +1,18 @@
+# This runs jobs which pyiron modules should run on release
+# This job runs on pull requests and does not actually publish anything to pypi
+# It is useful for debugging new build recipes
+# To actually release, change the `on` and `publish-to-pypi` fields
+name: Preview Release
+
+on:
+  pull_request:
+#  release:
+#    types: [ published ]
+
+jobs:
+  pyiron:
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit
+    with:
+      semantic-upper-bound: 'minor'
+      publish-to-pypi: false

.github/workflows/push-pull.yml

@@ -0,0 +1,13 @@
+# This runs jobs which pyiron modules should run on pushes or PRs to main
+
+name: Push-Pull
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  pyiron:
+    uses: pyiron/actions/.github/workflows/[email protected]
+    secrets: inherit

.github/workflows/pypicheck.yml

@@ -19,7 +19,7 @@ jobs:
         miniforge-variant: Mambaforge
         channel-priority: strict
         auto-update-conda: true  
-        environment-file: .ci_support/environment-pypi-unit.yml
+        environment-file: .ci_support/environment.yml
     - name: Setup
       shell: bash -l {0}
       run: |