Merge pull request #37 from openpathsampling/release-0.2.0

Release 0.2.0

Author: dwhswenson

.autorelease/test-testpypi.sh

@@ -0,0 +1,2 @@
+python -m pip install sqlalchemy dill pytest
+py.test --pyargs paths_cli

.github/workflows/autorelease-default-env.sh

@@ -1,4 +1,4 @@
-INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.3"
+INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.6"
 if [ -f autorelease-env.sh ]; then
     source autorelease-env.sh
 fi

.github/workflows/autorelease-deploy.yml

@@ -14,7 +14,9 @@ jobs:
           python-version: "3.x"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
-          cat autorelease-env.sh >> $GITHUB_ENV
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
           eval $INSTALL_AUTORELEASE
         name: "Install autorelease"
       - run: |
@@ -27,5 +29,5 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@master
         with:
           password: ${{ secrets.pypi_password }}
-        name: "Deploy to testpypi"
+        name: "Deploy to pypi"
 

.github/workflows/autorelease-gh-rel.yml

@@ -15,7 +15,9 @@ jobs:
           python-version: "3.7"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
-          cat autorelease-env.sh >> $GITHUB_ENV
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
           eval $INSTALL_AUTORELEASE
         name: "Install autorelease"
       - run: |

.github/workflows/autorelease-prep.yml

@@ -19,7 +19,9 @@ jobs:
           python-version: "3.x"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
-          cat autorelease-env.sh >> $GITHUB_ENV
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
           eval $INSTALL_AUTORELEASE
         name: "Install autorelease"
       - run: |
@@ -49,7 +51,9 @@ jobs:
           python-version: "3.x"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
-          cat autorelease-env.sh >> $GITHUB_ENV
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
           eval $INSTALL_AUTORELEASE
         name: "Install autorelease"
       - run: test-testpypi

README.md

@@ -22,6 +22,7 @@ miscellaneous operations on OPS output files.
 **Simulation Commands:**
 
 * `visit-all`:     Run MD to generate initial trajectories
+* `md`:            Run MD for fixed time or until a given ensemble is satisfied
 * `equilibrate`:   Run equilibration for path sampling
 * `pathsampling`:  Run any path sampling simulation, including TIS variants
 

autorelease-env.sh

@@ -1,2 +1,2 @@
-INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.3 nose"
+INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.3 nose sqlalchemy dill"
 PACKAGE_IMPORT_NAME=paths_cli

devtools/tests_require.txt

@@ -3,3 +3,6 @@ nose
 pytest
 pytest-cov
 coveralls
+# following are for SimStore integration
+dill
+sqlalchemy

paths_cli/commands/contents.py

@@ -1,19 +1,64 @@
 import click
 from paths_cli.parameters import INPUT_FILE
 
+UNNAMED_SECTIONS = ['steps', 'movechanges', 'samplesets', 'trajectories',
+                    'snapshots']
+
+NAME_TO_ATTR = {
+    'CVs': 'cvs',
+    'Volumes': 'volumes',
+    'Engines': 'engines',
+    'Networks': 'networks',
+    'Move Schemes': 'schemes',
+    'Simulations': 'pathsimulators',
+    'Tags': 'tags',
+    'Steps': 'steps',
+    'Move Changes': 'movechanges',
+    'SampleSets': 'samplesets',
+    'Trajectories': 'trajectories',
+    'Snapshots': 'snapshots'
+}
+
 @click.command(
     'contents',
     short_help="list named objects from an OPS .nc file",
 )
 @INPUT_FILE.clicked(required=True)
-def contents(input_file):
+@click.option('--table', type=str, required=False,
+              help="table to show results from")
+def contents(input_file, table):
     """List the names of named objects in an OPS .nc file.
 
     This is particularly useful when getting ready to use one of simulation
     scripts (i.e., to identify exactly how a state or engine is named.)
     """
     storage = INPUT_FILE.get(input_file)
     print(storage)
+    if table is None:
+        report_all_tables(storage)
+    else:
+        table_attr = table.lower()
+        try:
+            store = getattr(storage, table_attr)
+        except AttributeError:
+            raise click.UsageError("Unknown table: '" + table_attr + "'")
+        else:
+            print(get_section_string(table_attr, store))
+
+
+def get_section_string(label, store):
+    attr = NAME_TO_ATTR.get(label, label.lower())
+    if attr in UNNAMED_SECTIONS:
+        string = get_unnamed_section_string(label, store)
+    elif attr in ['tag', 'tags']:
+        string = get_section_string_nameable(label, store, _get_named_tags)
+    else:
+        string = get_section_string_nameable(label, store,
+                                             _get_named_namedobj)
+    return string
+
+
+def report_all_tables(storage):
     store_section_mapping = {
         'CVs': storage.cvs, 'Volumes': storage.volumes,
         'Engines': storage.engines, 'Networks': storage.networks,
@@ -26,12 +71,16 @@ def contents(input_file):
     print(get_section_string_nameable('Tags', storage.tags, _get_named_tags))
 
     print("\nData Objects:")
-    unnamed_sections = {
-        'Steps': storage.steps, 'Move Changes': storage.movechanges,
-        'SampleSets': storage.samplesets,
-        'Trajectories': storage.trajectories, 'Snapshots': storage.snapshots
+    data_object_mapping = {
+        'Steps': lambda storage: storage.steps,
+        'Move Changes': lambda storage: storage.movechanges,
+        'SampleSets': lambda storage: storage.samplesets,
+        'Trajectories': lambda storage: storage.trajectories,
+        'Snapshots': lambda storage: storage.snapshots
     }
-    for section, store in unnamed_sections.items():
+
+    for section, store_func in data_object_mapping.items():
+        store = store_func(storage)
         print(get_unnamed_section_string(section, store))
 
 def _item_or_items(count):

paths_cli/commands/equilibrate.py

@@ -43,6 +43,7 @@ def equilibrate_main(output_storage, scheme, init_conds, multiplier,
                      extra_steps):
     import openpathsampling as paths
     init_conds = scheme.initial_conditions_from_trajectories(init_conds)
+    scheme.assert_initial_conditions(init_conds)
     simulation = paths.PathSampling(
         storage=output_storage,
         move_scheme=scheme,