New SEAMM package database

0. gaussian-step changed from 2024.12.1.1 to 2024.12.9 1. mopac-step changed from 2024.10.15 to 2024.12.9 2. psi4-step changed from 2024.10.15 to 2024.12.7 3. read-structure-step changed from 2024.11.29 to 2024.12.7 4. molsystem changed from 2024.11.27.1 to 2024.12.7 5. subflowchart-step changed from 3rd-party plug-in to MolSSI plug-in 6. structure-step changed from 2024.10.24 to 2024.10.20 7. structure-step changed from 3rd-party plug-in to MolSSI plug-in 8. seamm-geometric changed from 3rd-party plug-in to Core package 9. diffusivity-step changed from 2024.7.30.1 to 2024.7.30 10. crystal-builder-step changed from 2022.7.31 to 2022.8.1 11. seamm-ff-util changed from 2024.6.27 (conda-forge) to 2024.6.28 (pypi) 12. seamm-dashboard changed from Core package to 3rd-party plug-in
molssi-seamm · Dec 10, 2024 · 6e9e373 · 6e9e373
1 parent 64c9434
commit 6e9e373
Show file tree

Hide file tree

Showing 9 changed files with 188 additions and 59 deletions.
diff --git a/.github/workflows/Check.yaml b/.github/workflows/Check.yaml
@@ -1,9 +1,9 @@
 name: Check
 
 on:
-  schedule:
-    - cron: '0 5 * * *'
   workflow_dispatch:
+  # schedule:
+  #   - cron: '0 5 * * *'
 
 jobs:
   check:

diff --git a/README.rst b/README.rst
@@ -7,11 +7,29 @@ Tools to create packing lists and packages for the SEAMM environment.
 * Documentation: https://molssi-seamm.github.io
 * Code: https://github.com/molssi-seamm/packaging
 
-Features
---------
+HOWTO
+-----
 
-* TODO
+The automated packaging system is designed to create a package for the SEAMM
+environment using GitHub Actions. However, this is currently not working because PyPi
+has restricted programmatic access to the API. The following instructions are for
+running by hand.
 
+#. Clone the repository and ensure it is up to date
+#. From the PyPi website search for "seamm" and save the pages as "search1.html",
+   "search2.html", etc. in the Downloads directory
+#. Run the script in the top level of the project:
+
+   .. code-block:: bash
+
+       python -m seamm_packaging
+
+   This should update the package info and upload it to Zenodo.
+
+#. Push the changes to the repository
+#. Make a new release
+#. Manually invoke the GitHub Action "Release" to do the rest.
+
 seamm Docker image
 ------------------------
 There is a Docker image available for SEAMM. It is available at the Github Container

diff --git a/environments/SEAMM_packages.json b/environments/SEAMM_packages.json
@@ -1,7 +1,7 @@
 {
     "conceptdoi": "10.5281/zenodo.7789853",
-    "date": "2024-12-02T05:41:08.909305+00:00",
-    "doi": "10.5281/zenodo.14257716",
+    "date": "2024-12-10T16:13:48.379586+00:00",
+    "doi": "10.5281/zenodo.14363822",
     "packages": {
         "control-parameters-step": {
             "channel": "pypi",
@@ -13,7 +13,7 @@
             "channel": "pypi",
             "description": "A SEAMM plug-in for creating crystals from prototypes, including Strukturbericht designations.",
             "type": "MolSSI plug-in",
-            "version": "2022.7.31"
+            "version": "2022.8.1"
         },
         "custom-step": {
             "channel": "pypi",
@@ -31,7 +31,7 @@
             "channel": "pypi",
             "description": "A SEAMM plug-in for Diffusivity",
             "type": "MolSSI plug-in",
-            "version": "2024.7.30.1"
+            "version": "2024.7.30"
         },
         "energy-scan-step": {
             "channel": "pypi",
@@ -61,7 +61,7 @@
             "channel": "pypi",
             "description": "A SEAMM plugin for A SEAMM plug-in for Gaussian",
             "type": "MolSSI plug-in",
-            "version": "2024.12.1.1"
+            "version": "2024.12.9"
         },
         "geometry-analysis-step": {
             "channel": "pypi",
@@ -85,13 +85,13 @@
             "channel": "conda-forge",
             "description": "molsystem",
             "type": "Core package",
-            "version": "2024.11.27.1"
+            "version": "2024.12.7"
         },
         "mopac-step": {
             "channel": "pypi",
             "description": "A SEAMM plug-in to setup, run and analyze semiempirical calculations with MOPAC",
             "type": "MolSSI plug-in",
-            "version": "2024.10.15"
+            "version": "2024.12.9"
         },
         "packmol-step": {
             "channel": "pypi",
@@ -109,7 +109,7 @@
             "channel": "pypi",
             "description": "A SEAMM plug-in to setup, run and analyze quantum chemistry calculations using Psi4",
             "type": "MolSSI plug-in",
-            "version": "2024.10.15"
+            "version": "2024.12.7"
         },
         "pyxtal-step": {
             "channel": "pypi",
@@ -139,13 +139,7 @@
             "channel": "pypi",
             "description": "A SEAMM plug-in to read common formats in computational chemistry",
             "type": "MolSSI plug-in",
-            "version": "2024.11.29"
-        },
-        "reference-handler": {
-            "channel": "conda-forge",
-            "description": "no description given",
-            "type": "Core package",
-            "version": "0.9.1"
+            "version": "2024.12.7"
         },
         "seamm": {
             "channel": "conda-forge",
@@ -162,7 +156,7 @@
         "seamm-dashboard": {
             "channel": "conda-forge",
             "description": "The Web Dashboard for SEAMM (Simulation Environment for Atomistic and Molecular Simulations).",
-            "type": "Core package",
+            "type": "3rd-party plug-in",
             "version": "2024.6.2"
         },
         "seamm-datastore": {
@@ -178,15 +172,15 @@
             "version": "2024.7.25"
         },
         "seamm-ff-util": {
-            "channel": "conda-forge",
+            "channel": "pypi",
             "description": "seamm_ff_util",
             "type": "Core package",
-            "version": "2024.6.27"
+            "version": "2024.6.28"
         },
         "seamm-geometric": {
             "channel": "pypi",
             "description": "geomeTRIC connector for SEAMM",
-            "type": "3rd-party plug-in",
+            "type": "Core package",
             "version": "2024.10.20"
         },
         "seamm-installer": {
@@ -228,13 +222,13 @@
         "structure-step": {
             "channel": "pypi",
             "description": "A SEAMM plug-in for energy optimized structures",
-            "type": "3rd-party plug-in",
-            "version": "2024.10.24"
+            "type": "MolSSI plug-in",
+            "version": "2024.10.20"
         },
         "subflowchart-step": {
             "channel": "pypi",
             "description": "A SEAMM plug-in for subflowcharts",
-            "type": "3rd-party plug-in",
+            "type": "MolSSI plug-in",
             "version": "2024.11.18"
         },
         "supercell-step": {

diff --git a/environments/seamm.yml b/environments/seamm.yml
@@ -15,23 +15,23 @@ dependencies:
   - qcportal
 
   - molsystem
-  - reference-handler
   - seamm
-  - seamm-dashboard
   - seamm-datastore
-  - seamm-ff-util
   - seamm-installer
   - seamm-util
   - seamm-widgets
 
     # MolSSI plug-ins
 
     # 3rd-party plug-ins
+  - seamm-dashboard
 
     # PyPi packages
   - pip:
     # Core packages
     - seamm-exec
+    - seamm-ff-util
+    - seamm-geometric
     - seamm-jobserver
 
     # MolSSI plug-ins
@@ -58,14 +58,13 @@ dependencies:
     - read-structure-step
     - set-cell-step
     - strain-step
+    - structure-step
+    - subflowchart-step
     - supercell-step
     - table-step
     - thermal-conductivity-step
     - torchani-step
 
     # 3rd-party plug-ins
     - pyxtal-step
-    - seamm-ase
-    - seamm-geometric
-    - structure-step
-    - subflowchart-step
+    - seamm-ase
diff --git a/environments/seamm_pinned.yml b/environments/seamm_pinned.yml
@@ -16,58 +16,57 @@ dependencies:
 
 
 # Core packages
-  - molsystem==2024.11.27.1
-  - reference-handler==0.9.1
+  - molsystem==2024.12.7
   - seamm==2024.11.29
-  - seamm-dashboard==2024.6.2
   - seamm-datastore==2024.6.2
-  - seamm-ff-util==2024.6.27
   - seamm-installer==2024.4.22
   - seamm-util==2024.8.22
   - seamm-widgets==2024.10.10
 
     # MolSSI plug-ins
 
     # 3rd-party plug-ins
+  - seamm-dashboard==2024.6.2
 
     # PyPi packages
   - pip:
     # Core packages
     - seamm-exec==2024.7.25
+    - seamm-ff-util==2024.6.28
+    - seamm-geometric==2024.10.20
     - seamm-jobserver==2024.3.12
 
     # MolSSI plug-ins
     - control-parameters-step==2023.11.15
-    - crystal-builder-step==2022.7.31
+    - crystal-builder-step==2022.8.1
     - custom-step==2023.12.12
     - dftbplus-step==2024.10.20
-    - diffusivity-step==2024.7.30.1
+    - diffusivity-step==2024.7.30
     - energy-scan-step==2024.5.23
     - fhi-aims-step==2024.10.31
     - forcefield-step==2024.6.30
     - from-smiles-step==2024.10.31
-    - gaussian-step==2024.12.1.1
+    - gaussian-step==2024.12.9
     - geometry-analysis-step==2023.1.14
     - lammps-step==2024.8.22
     - loop-step==2024.11.19
-    - mopac-step==2024.10.15
+    - mopac-step==2024.12.9
     - packmol-step==2024.7.25
     - properties-step==2023.7.31
-    - psi4-step==2024.10.15
+    - psi4-step==2024.12.7
     - qcarchive-step==2023.3.30
     - quickmin-step==2024.5.7
     - rdkit-step==2023.2.22
-    - read-structure-step==2024.11.29
+    - read-structure-step==2024.12.7
     - set-cell-step==2021.10.14
     - strain-step==2022.11.7
+    - structure-step==2024.10.20
+    - subflowchart-step==2024.11.18
     - supercell-step==2023.11.5
     - table-step==2023.11.10
     - thermal-conductivity-step==2024.6.3
     - torchani-step==2024.10.15
 
     # 3rd-party plug-ins
     - pyxtal-step==2021.7.29
-    - seamm-ase==2024.10.20
-    - seamm-geometric==2024.10.20
-    - structure-step==2024.10.24
-    - subflowchart-step==2024.11.18
+    - seamm-ase==2024.10.20
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,7 +18,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
 ]
-requires-python = ">=3.12"
+# requires-python = ">=3.12"
 # Declare any run-time dependencies that should be installed with the package.
 dependencies = [
     "requests",

diff --git a/seamm_packaging/__main__.py b/seamm_packaging/__main__.py
@@ -4,11 +4,12 @@
 from .packaging import find_packages, create_env_files, upload_to_zenodo
 
 if __name__ == "__main__":
-    changed, packages = find_packages()
-    if changed:
-        print("Packages have changed, updating environment files")
-        create_env_files(packages)
+    if False:
+        changed, packages = find_packages()
+        if changed:
+            print("Packages have changed, updating environment files")
+            create_env_files(packages)
 
-        print("Uploading to ZENODO")
-        doi = upload_to_zenodo()
-        print(f"   new DOI = {doi}")
+    print("Uploading to ZENODO")
+    doi = upload_to_zenodo()
+    print(f"   new DOI = {doi}")