Merge pull request #90 from OpenBioSim/fix_88

Fix issue #88 [ci skip]
michellab · Jun 5, 2023 · a68f7c2 · a68f7c2
2 parents 28af3ed + 7d6db72
commit a68f7c2
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Showing 3 changed files with 26 additions and 3 deletions.
diff --git a/doc/source/contributing/development.rst b/doc/source/contributing/development.rst
@@ -142,6 +142,29 @@ Instead use:
    print(c.getList())
    [1, 2, 3, 4, 5]
 
+Sire
+----
+
+BioSimSpace is built on top of the `Sire <https://github.com/openbiosim/sire>`__
+and makes exstensive use of its API. Sire has recently been updated to a new,
+Python compliant API. Within BioSimSpace, Sire is currently imported in a
+*mixed* mode so that we can use *both* the new and legacy APIs while we
+work to port things over. A consequence of this is that Sire imports
+*must* follow those for BioSimSpace, e.g.:
+
+.. code-block:: python
+
+     from sire.mol import AtomIdx
+     import BioSimSpace as BSS
+
+will fail, while the following will work:
+
+.. code-block:: python
+
+     import BioSimSpace as BSS
+     from sire.mol import AtomIdx
+
+
 Workflow
 ========
 

diff --git a/nodes/playground/prepareFEP.ipynb b/nodes/playground/prepareFEP.ipynb
@@ -25,8 +25,8 @@
    "source": [
     "import os\n",
     "import zipfile\n",
-    "from sire.legacy.Mol import AtomIdx\n",
-    "import BioSimSpace as BSS"
+    "import BioSimSpace as BSS\n",
+    "from sire.legacy.Mol import AtomIdx"
    ]
   },
   {

diff --git a/nodes/playground/prepareFEP.py b/nodes/playground/prepareFEP.py
@@ -13,8 +13,8 @@
 
 import os
 import zipfile
-from sire.legacy.Mol import AtomIdx
 import BioSimSpace as BSS
+from sire.legacy.Mol import AtomIdx
 
 
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