Merge pull request #18 from molssi-seamm/system2

Updated to be compatible with the new system classes.
molssi-seamm · Feb 4, 2021 · 45eb4df · 45eb4df
2 parents e5a4d3a + 6446df0
commit 45eb4df
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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 +50,4 @@ 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 packmol_step tests
         yapf --diff --recursive packmol_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]

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 packmol_step tests
         yapf --diff --recursive packmol_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]
@@ -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
@@ -2,8 +2,12 @@
 packmol step
 ============
 
-.. image:: https://img.shields.io/travis/molssi-seamm/packmol_step.svg
-   :target: https://travis-ci.org/molssi-seamm/packmol_step
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/packmol_step
+   :target: https://github.com/molssi-seamm/packmol_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/packmol_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/packmol_step/actions
    :alt: Build Status
 
 .. image:: https://codecov.io/gh/molssi-seamm/packmol_step/branch/master/graph/badge.svg
@@ -14,8 +18,8 @@ packmol step
    :target: https://lgtm.com/projects/g/molssi-seamm/packmol_step/context:python
    :alt: Code Quality
 
-.. image:: https://readthedocs.org/projects/packmol-step/badge/?version=latest
-   :target: https://packmol-step.readthedocs.io/en/latest/?badge=latest
+.. image:: https://github.com/molssi-seamm/packmol_step/workflows/Documentation/badge.svg
+   :target: https://molssi-seamm.github.io/packmol_step/index.html
    :alt: Documentation Status
 
 .. image:: https://pyup.io/repos/github/molssi-seamm/packmol_step/shield.svg
@@ -30,7 +34,7 @@ A step for a SEAMM flowchart for building periodic fluid boxes using Packmol
 
 
 * Free software: BSD license
-* Documentation: https://packmol-step.readthedocs.io.
+* Documentation: https://molssi-seamm.github.io/packmol_step/index.html
 
 
 Features

diff --git a/packmol_step/packmol.py b/packmol_step/packmol.py
@@ -134,8 +134,8 @@ def run(self):
         next_node = super().run(printer)
 
         # Get the system
-        systems = self.get_variable('_systems')
-        system = self.get_variable('_system')
+        system_db = self.get_variable('_system_db')
+        configuration = system_db.system.configuration
 
         # The options from command line, config file ...
         path = self.options['packmol_path']
@@ -193,7 +193,7 @@ def run(self):
             )
 
         tmp = self.calculate(
-            system,
+            configuration,
             size=size,
             volume=volume,
             density=density,
@@ -217,7 +217,7 @@ def run(self):
         lines.append('end structure')
         lines.append('')
 
-        files = {'input.pdb': system.to_pdb_text()}
+        files = {'input.pdb': configuration.to_pdb_text()}
         files['input.inp'] = '\n'.join(lines)
 
         self.logger.log(0, pprint.pformat(files))
@@ -239,15 +239,17 @@ def run(self):
         # need to graft to the original structure.
 
         # Create a new, temporary system and get the coordinates
-        tmp_sys = systems.create_system('tmp_sys', temporary=True)
-        tmp_sys.from_pdb_text(result['packmol.pdb']['data'])
-        n_atoms = tmp_sys.n_atoms()
-        xs = [*tmp_sys.atoms['x']]
-        ys = [*tmp_sys.atoms['y']]
-        zs = [*tmp_sys.atoms['z']]
-        del systems['tmp_sys']
-
-        n_atoms_per_molecule = system.n_atoms()
+        tmp_sys = system_db.create_system('tmp_sys', make_current=False)
+        tmp_configuration = tmp_sys.create_configuration('tmp')
+        tmp_configuration.from_pdb_text(result['packmol.pdb']['data'])
+        tmp_atoms = tmp_configuration.atoms
+        n_atoms = tmp_atoms.n_atoms
+        xs = [*tmp_atoms['x']]
+        ys = [*tmp_atoms['y']]
+        zs = [*tmp_atoms['z']]
+        system_db.delete_system(tmp_sys)
+
+        n_atoms_per_molecule = configuration.n_atoms
         if n_atoms_per_molecule * n_molecules != n_atoms:
             raise RuntimeError(
                 'Serious problem in Packmol with the number of atoms'
@@ -256,47 +258,35 @@ def run(self):
                 )
             )
 
-        # get the initial atoms so that we can duplicate them
-        rows = system.atoms.atoms()
-        atom_data = {}
-        columns = [x[0] for x in rows.description]
-        for column in columns:
-            atom_data[column] = []
-        for row in rows:
-            for column, value in zip(columns, row):
-                atom_data[column].append(value)
-        atom_ids = atom_data['id']
+        # Get a copy of the current atom and bond data
+        atoms = configuration.atoms
+        atom_data = atoms.get_as_dict()
+        # index of atoms to use for bonds
+        index = {j: i for i, j in enumerate(atom_data['id'])}
         del atom_data['id']
-        to_index = {j: i for i, j in enumerate(atom_ids)}
-
-        # and bonds
-        rows = system.bonds.bonds()
-        bond_data = {}
-        columns = [x[0] for x in rows.description]
-        for column in columns:
-            bond_data[column] = []
-        for row in rows:
-            for column, value in zip(columns, row):
-                bond_data[column].append(value)
-        i_index = [to_index[i] for i in bond_data['i']]
-        j_index = [to_index[j] for j in bond_data['j']]
+        bonds = configuration.bonds
+        bond_data = bonds.get_as_dict()
+        del bond_data['id']
+
+        i_index = [index[i] for i in bond_data['i']]
+        j_index = [index[j] for j in bond_data['j']]
 
         # Append the atoms and bonds n_molecules-1 times to give n_molecules
         for copy in range(1, n_molecules):
-            new_atoms = system.atoms.append(**atom_data)
+            new_atoms = configuration.atoms.append(**atom_data)
 
             bond_data['i'] = [new_atoms[i] for i in i_index]
             bond_data['j'] = [new_atoms[j] for j in j_index]
-            system.bonds.append(**bond_data)
+            configuration.bonds.append(**bond_data)
 
         # And set the coordinates to the correct ones
-        system.atoms['x'] = xs
-        system.atoms['y'] = ys
-        system.atoms['z'] = zs
+        configuration.atoms['x'] = xs
+        configuration.atoms['y'] = ys
+        configuration.atoms['z'] = zs
 
         # make periodic of correct size
-        system.periodicity = 3
-        system.cell.set_cell(size, size, size, 90.0, 90.0, 90.0)
+        configuration.periodicity = 3
+        configuration.cell.parameters = (size, size, size, 90.0, 90.0, 90.0)
 
         string = 'Created a cubic cell {size:.5~P} on a side'
         string += ' with {n_molecules} molecules'
@@ -326,7 +316,7 @@ def run(self):
 
     def calculate(
         self,
-        system,
+        configuration,
         size=None,
         volume=None,
         density=None,
@@ -337,13 +327,13 @@ def calculate(
     ):
         """Work out the other variables given any two independent ones"""
 
-        if system.n_atoms() == 0:
+        if configuration.n_atoms == 0:
             self.logger.error('Packmol calculate: there is no structure!')
             raise RuntimeError('Packmol calculate: there is no structure!')
 
-        elements = system.atoms.symbols()
+        elements = configuration.atoms.symbols
         n_atoms_per_molecule = len(elements)
-        molecular_mass = system.mass() * ureg.g / ureg.mol  # g/mol
+        molecular_mass = configuration.mass * ureg.g / ureg.mol  # g/mol
         molecular_mass.ito('kg')
 
         n_parameters = 0

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