Merge pull request #9 from molssi-seamm/system2

Updated for compatibility with the new system classes.
molssi-seamm · Feb 4, 2021 · 7f3de62 · 7f3de62
2 parents 4577dee + dd0968e
commit 7f3de62
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diff --git a/.github/workflows/BranchCI.yaml b/.github/workflows/BranchCI.yaml
@@ -4,7 +4,6 @@ on:
   push:
     branches-ignore:
       - 'main'
-      - 'master'
 
 jobs:
   light-ci:
@@ -51,10 +50,5 @@ jobs:
         file: ./coverage.xml
         flags: unittests
         name: codecov-ubuntu-latest-py3.8
-    - name: Build documentation
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      shell: bash -l {0}
-      run: |
-        docs/buildDocs.sh
+
 
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -1,26 +1,21 @@
 name: CI
 
 on:
-  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
   push:
     branches:
-      - "master"
       - "main"
   pull_request:
     branches:
-      - "master"
       - "main"
   schedule:
-    # Run on master by default Sunday morning at 3:30:
+    # Run by default Sunday morning at 3:30:
     #   Scheduled workflows run on the latest commit on the default or base branch.
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "30 3 * * 0"
 
 jobs:
-  lint-docs:
-    name: Lint-Docs ubuntu-latest Py3.8
+  lint:
+    name: Lint ubuntu-latest Py3.8
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v1
@@ -53,17 +48,11 @@ jobs:
       run: |
         flake8 psi4_step tests
         yapf --diff --recursive psi4_step tests
-    - name: Build documentation
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      shell: bash -l {0}
-      run: |
-        docs/buildDocs.sh
 
   test:
     name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
-    needs: lint-docs
+    needs: lint
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]

diff --git a/.github/workflows/Docs.yaml b/.github/workflows/Docs.yaml
@@ -0,0 +1,40 @@
+name: Documentation
+
+on: push
+
+jobs:
+  docs:
+    name: Docs ubuntu-latest Py3.8
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        # This gets all branches (1 = only current branch)
+        fetch-depth: 0
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+    # More info on options: https://github.com/conda-incubator/setup-miniconda
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: 3.8
+        environment-file: devtools/conda-envs/test_env.yaml
+        activate-environment: test
+        auto-update-conda: false
+        auto-activate-base: false
+        show-channel-urls: true
+    - name: Install package
+      # conda setup requires this special shell
+      shell: bash -l {0}
+      run: |
+        python -m pip install . --no-deps
+        conda list
+    - name: Build documentation
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      shell: bash -l {0}
+      run: |
+        docs/buildDocs.sh
diff --git a/.github/workflows/Release.yaml b/.github/workflows/Release.yaml
@@ -1,18 +1,14 @@
 name: Release
 
 on:
-  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
   release:
     types: [published]
     branches:
-      - "master"
       - "main"
 
 jobs:
-  lint-docs:
-    name: Lint-Docs ubuntu-latest Py3.8
+  lint:
+    name: Lint ubuntu-latest Py3.8
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v1
@@ -45,17 +41,11 @@ jobs:
       run: |
         flake8 psi4_step tests
         yapf --diff --recursive psi4_step tests
-    - name: Build documentation
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      shell: bash -l {0}
-      run: |
-        docs/buildDocs.sh
 
   test:
     name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
-    needs: lint-docs
+    needs: lint
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
@@ -98,7 +88,7 @@ jobs:
     # only to test.pypi, otherwise to both it and the main pypi.
     if: github.event_name == 'release' && startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
-    needs: [lint-docs, test]
+    needs: [lint, test]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python 3.8

diff --git a/README.rst b/README.rst
@@ -2,30 +2,39 @@
 Psi4 Step
 =========
 
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/psi4_step
+   :target: https://github.com/molssi-seamm/psi4_step/pulls
+   :alt: GitHub pull requests
 
-.. image:: https://img.shields.io/travis/molssi-seamm/psi4_step.svg
-   :target: https://travis-ci.org/molssi-seamm/psi4_step
-.. image:: https://pyup.io/repos/github/molssi-seamm/psi4_step/shield.svg
-   :target: https://pyup.io/repos/github/molssi-seamm/psi4_step/
-      :alt: Updates
-
+.. image:: https://github.com/molssi-seamm/psi4_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/psi4_step/actions
+   :alt: Build Status
 
 .. image:: https://codecov.io/gh/molssi-seamm/psi4_step/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/molssi-seamm/psi4_step
+   :alt: Code Coverage
+
+.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/psi4_step.svg?logo=lgtm&logoWidth=18
+   :target: https://lgtm.com/projects/g/molssi-seamm/psi4_step/context:python
+   :alt: Code Quality
 
-.. image:: https://readthedocs.org/projects/psi4-step/badge/?version=latest
-   :target: https://psi4-step.readthedocs.io/en/latest/?badge=latest
-      :alt: Documentation Status
+.. image:: https://github.com/molssi-seamm/psi4_step/workflows/Documentation/badge.svg
+   :target: https://molssi-seamm.github.io/psi4_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://pyup.io/repos/github/molssi-seamm/psi4_step/shield.svg
+   :target: https://pyup.io/repos/github/molssi-seamm/psi4_step/
+   :alt: Updates for Dependencies
 
 .. image:: https://img.shields.io/pypi/v/psi4_step.svg
    :target: https://pypi.python.org/pypi/psi4_step
-
+   :alt: PyPi VERSION
 
 A step for Psi4 in a SEAMM flowchart
 
 
 * Free software: BSD-3-Clause
-* Documentation: https://psi4-step.readthedocs.io.
+* Documentation: https://molssi-seamm.github.io/psi4_step/index.html
 
 
 Features

diff --git a/psi4_step/psi4.py b/psi4_step/psi4.py
@@ -324,8 +324,9 @@ def run(self):
         printer.important(self.header)
         printer.important('')
 
-        system = self.get_variable('_system')
-        n_atoms = system.n_atoms()
+        system_db = self.get_variable('_system_db')
+        configuration = system_db.system.configuration
+        n_atoms = configuration.n_atoms
         if n_atoms == 0:
             self.logger.error('Psi4 run(): there is no structure!')
             raise RuntimeError('Psi4 run(): there is no structure!')
@@ -525,7 +526,8 @@ def analyze(self, indent='', **kwargs):
             with structure_file.open(mode='r') as fd:
                 structure = json.load(fd)
         if 'geom' in structure:
-            system = self.get_variable('_system')
+            system_db = self.get_variable('_system_db')
+            configuration = system_db.system.configuration
             xs = []
             ys = []
             zs = []
@@ -534,9 +536,9 @@ def analyze(self, indent='', **kwargs):
                 xs.append(x)
                 ys.append(next(it))
                 zs.append(next(it))
-            system.atoms['x'][0:] = xs
-            system.atoms['y'][0:] = ys
-            system.atoms['z'][0:] = zs
+            configuration.atoms['x'][0:] = xs
+            configuration.atoms['y'][0:] = ys
+            configuration.atoms['z'][0:] = zs
             printer.important(
                 self.indent +
                 '    Updated the system with the structure from Psi4',
@@ -546,7 +548,8 @@ def analyze(self, indent='', **kwargs):
     def _convert_structure(self, name=None):
         """Convert the structure to the input for Psi4."""
 
-        system = self.get_variable('_system')
+        system_db = self.get_variable('_system_db')
+        configuration = system_db.system.configuration
 
         structure = []
         if name is None:
@@ -555,40 +558,13 @@ def _convert_structure(self, name=None):
             structure.append('molecule ' + name + ' {')
 
         # Charge and multiplicity
-        if 'extras' in system:
-            extras = system['extras']
-
-            if 'open' in extras and extras['open'] is not None:
-                openshell = extras['open']
-                if (
-                    (
-                        isinstance(openshell, tuple) or
-                        isinstance(openshell, list)
-                    ) and len(openshell) > 1
-                ):
-                    nopen = openshell[0]
-                    norbitals = openshell[1]
-                    if nopen != norbitals:
-                        raise NotImplementedError(
-                            f"Handling of open shell = '{openshell}'"
-                        )
-                else:
-                    nopen = openshell
-                    norbitals = nopen
-
-                if 'net_charge' in extras and extras['net_charge'] is not None:
-                    structure.append(f"    {extras['net_charge']}   {nopen}")
-                else:
-                    structure.append(f'    0   {nopen}')
-            else:
-                if 'net_charge' in extras and extras['net_charge'] is not None:
-                    structure.append(f"    {extras['net_charge']}   1")
+        # not handled yet!!!!
 
-        elements = system.atoms.symbols()
-        coordinates = system.atoms.coordinates()
+        elements = configuration.atoms.symbols
+        coordinates = configuration.atoms.coordinates
 
-        if 'freeze' in system.atoms:
-            freeze = system.atoms['freeze']
+        if 'freeze' in configuration.atoms:
+            freeze = configuration.atoms['freeze']
         else:
             freeze = [''] * len(elements)
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,2 @@
 psutil==5.7.2
-seamm==2020.12.4
+seamm==2021.2.2