Merge pull request #16 from molssi-seamm/system2

Updated to be compatible with the new system classes.
molssi-seamm · Feb 4, 2021 · afa442c · afa442c
2 parents 8bb5854 + 002e6db
commit afa442c
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Showing 7 changed files with 76 additions and 56 deletions.
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 +50,3 @@ 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 on main 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 loop_step tests
         yapf --diff --recursive loop_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 loop_step tests
         yapf --diff --recursive loop_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
@@ -2,24 +2,33 @@
 Loop Step
 =========
 
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/loop_step
+   :target: https://github.com/molssi-seamm/loop_step/pulls
+   :alt: GitHub pull requests
 
-.. image:: https://img.shields.io/pypi/v/loop_step.svg
-        :target: https://pypi.python.org/pypi/loop_step
+.. image:: https://github.com/molssi-seamm/loop_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/loop_step/actions
+   :alt: Build Status
 
-.. image:: https://img.shields.io/travis/molssi-seamm/loop_step.svg
-        :target: https://travis-ci.org/molssi-seamm/loop_step
+.. image:: https://codecov.io/gh/molssi-seamm/loop_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/loop_step
+   :alt: Code Coverage
 
-.. image:: https://readthedocs.org/projects/loop-step/badge/?version=latest
-        :target: https://loop-step.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
+.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/loop_step.svg?logo=lgtm&logoWidth=18
+   :target: https://lgtm.com/projects/g/molssi-seamm/loop_step/context:python
+   :alt: Code Quality
 
-.. image:: https://pyup.io/repos/github/molssi-seamm/loop_step/shield.svg
-     :target: https://pyup.io/repos/github/molssi-seamm/loop_step/
-     :alt: Updates
+.. image:: https://github.com/molssi-seamm/loop_step/workflows/Documentation/badge.svg
+   :target: https://molssi-seamm.github.io/loop_step/index.html
+   :alt: Documentation Status
 
-.. image:: https://codecov.io/gh/molssi-seamm/loop_step/branch/master/graph/badge.svg
-  :target: https://codecov.io/gh/molssi-seamm/loop_step
+.. image:: https://pyup.io/repos/github/molssi-seamm/loop_step/shield.svg
+   :target: https://pyup.io/repos/github/molssi-seamm/loop_step/
+   :alt: Updates for Dependencies
 
+.. image:: https://img.shields.io/pypi/v/loop_step.svg
+   :target: https://pypi.python.org/pypi/loop_step
+   :alt: PyPi VERSION
 
 Handle various type of loops in a SEAMM Flowchart
 

diff --git a/loop_step/loop.py b/loop_step/loop.py
@@ -8,7 +8,6 @@
 
 import loop_step
 import seamm
-from seamm_util import ureg, Q_, units_class  # noqa: F401
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
 
@@ -349,16 +348,17 @@ def run(self):
 
     def write_final_structure(self):
         """Write the final structure"""
-        system = self.get_variable('_system')
-        if system.n_atoms() > 0:
+        system_db = self.get_variable('_system_db')
+        configuration = system_db.system.configuration
+        if configuration.n_atoms > 0:
             # MMCIF file has bonds
             filename = os.path.join(
                 self.directory, f'iter_{self._loop_value}',
                 'final_structure.mmcif'
             )
             text = None
             try:
-                text = system.to_mmcif_text()
+                text = configuration.to_mmcif_text()
             except Exception:
                 message = (
                     'Error creating the mmcif file at the end of the loop\n\n'
@@ -371,14 +371,14 @@ def write_final_structure(self):
                     print(text, file=fd)
 
             # CIF file has cell
-            if system.periodicity == 3:
+            if configuration.periodicity == 3:
                 filename = os.path.join(
                     self.directory, f'iter_{self._loop_value}',
                     'final_structure.cif'
                 )
                 text = None
                 try:
-                    text = system.to_cif_text()
+                    text = configuration.to_cif_text()
                 except Exception:
                     message = (
                         'Error creating the cif file at the end of the loop'

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