From e41c20c591e0c40d7a70cf494c54e995089971ed Mon Sep 17 00:00:00 2001
From: ojeda-e <estefania.barretooje@ucalgary.ca>
Date: Mon, 4 Jul 2022 17:54:54 -0400
Subject: [PATCH] Added initial AVS benchmark

---
 benchmarks/__init__.py          |  0
 benchmarks/asv.conf.json        | 47 +++++++++++++++++++++++++++++++++
 benchmarks/membranecurvature.py | 16 +++++++++++
 3 files changed, 63 insertions(+)
 create mode 100644 benchmarks/__init__.py
 create mode 100644 benchmarks/asv.conf.json
 create mode 100644 benchmarks/membranecurvature.py

diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/benchmarks/asv.conf.json b/benchmarks/asv.conf.json
new file mode 100644
index 0000000..b22713c
--- /dev/null
+++ b/benchmarks/asv.conf.json
@@ -0,0 +1,47 @@
+{
+    // The version of the config file format.  Do not change, unless
+    // you know what you are doing.
+    "version": 1,
+
+    // The name of the project being benchmarked
+    "project": "membranecurvature",
+
+    // The URL of the source code repository for the project being
+    // benchmarked
+    "repo": "..",
+    "dvcs": "git",
+    "repo_subdir":".",
+    "branches": ["main"],
+
+    // The base URL to show information about a particular commit.
+    "show_commit_url": "https://github.com/MDAnalysis/membrane-curvature/commit/",
+
+    // The Pythons you'd like to test against.  If not provided, defaults
+    // to the current version of Python used to run `asv`.
+    "pythons": ["3.8"],
+    // The matrix of dependencies to test.  Each key is the name of a
+    // package (in PyPI) and the values are version numbers.  An empty
+    // list indicates to just test against the default (latest)
+    // version.
+    "conda_channels": ["conda-forge"],
+    "matrix": {
+        "numpy": [],
+        "scipy": [],
+	    "pytest": [],
+        "MDAnalysisTests": [],
+    },
+    // The directory (relative to the current directory) that benchmarks are
+    // stored in.  If not provided, defaults to "benchmarks"
+    "benchmark_dir": ".",
+    // The directory (relative to the current directory) to cache the Python
+    // environments in.  If not provided, defaults to "env"
+    "env_dir": "virtualenv",
+    "environment_type": "conda",
+    // The directory (relative to the current directory) that raw benchmark
+    // results are stored in.  If not provided, defaults to "results".
+    "results_dir": "results",
+    // The directory (relative to the current directory) that the html tree
+    // should be written to.  If not provided, defaults to "html".
+    "html_dir": "html"
+
+}
\ No newline at end of file
diff --git a/benchmarks/membranecurvature.py b/benchmarks/membranecurvature.py
new file mode 100644
index 0000000..acfa98c
--- /dev/null
+++ b/benchmarks/membranecurvature.py
@@ -0,0 +1,16 @@
+import MDAnalysis as mda
+from membrane_curvature.tests.datafiles import GRO_PO4_SMALL
+from membrane_curvature.base import MembraneCurvature
+
+
+class MembraneCurvatureBenchmark():
+    """
+    Benchmark for MembraneCurvature class
+    """
+
+    def setup(self):
+        self.u = mda.Universe(GRO_PO4_SMALL)
+        self.sel = mda.select_atoms('name PO4')
+
+    def time_surface(self):
+        MembraneCurvature(self.u, select=self.sel).run()