Merge pull request #36 from chrisjonesBSU/remove_hoomd

remove hoomd 2 from environment file

.github/workflows/pytest.yml

@@ -40,6 +40,12 @@ jobs:
       shell: bash -l {0}
       run: python -m pytest -v -rs --cov=./ --cov-report=xml
 
+    - name: Test hoomd2 functions
+      shell: bash -l {0}
+      run: |
+        mamba install -c conda-forge hoomd=2
+        python -m pytest -v -rs -k test_xml_to_gsd --cov=./ --cov-report=xml --cov-append
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:

cmeutils/gsd_utils.py

@@ -2,8 +2,6 @@
 
 import freud
 import gsd.hoomd
-import hoomd
-import hoomd.deprecated
 import numpy as np
 
 
@@ -202,6 +200,14 @@ def xml_to_gsd(xmlfile, gsdfile):
     gsdfile : str
         Path to gsd file
     """
+    try:
+        import hoomd
+        import hoomd.deprecated
+    except ImportError:
+        raise ImportError(
+                "You must have hoomd version 2 installed to use xml_to_gsd()"
+        )
+
     hoomd.util.quiet_status()
     hoomd.context.initialize("")
     hoomd.deprecated.init.read_xml(xmlfile, restart=xmlfile)

cmeutils/tests/test_gsd.py

@@ -2,13 +2,24 @@
 
 import gsd.hoomd
 import numpy as np
+import packaging.version
 
 from base_test import BaseTest
 from cmeutils.gsd_utils import (
     get_type_position, get_molecule_cluster, get_all_types, _validate_inputs,
     snap_delete_types, xml_to_gsd
 )
 
+try:
+    import hoomd
+    if "version" in dir(hoomd):
+        hoomd_version = packaging.version.parse(hoomd.version.version)
+    else:
+        hoomd_version = packaging.version.parse(hoomd.__version__)
+    has_hoomd = True
+except ImportError:
+    has_hoomd = False
+
 
 class TestGSD(BaseTest):
     def test_get_type_position(self, gsdfile):
@@ -57,6 +68,10 @@ def test_snap_delete_types_bonded(self, snap_bond):
         new_snap = snap_delete_types(snap_bond, "A")
         assert "A" not in new_snap.particles.types
 
+    @pytest.mark.skipif(
+        not has_hoomd or hoomd_version.major != 2,
+        reason="HOOMD is not installed or is wrong version"
+    )
     def test_xml_to_gsd(self, tmp_path, p3ht_gsd, p3ht_xml):
         new_gsd = tmp_path / "new.gsd"
         xml_to_gsd(p3ht_xml, new_gsd)

environment.yml

@@ -4,7 +4,6 @@ channels:
 dependencies:
   - freud
   - gsd
-  - hoomd<3
   - numpy
   - pip
   - python=3.7