From 546ad85f80235ba2190d6ae72b3e5007d30439ae Mon Sep 17 00:00:00 2001
From: Marcello Sega <marcello.sega@gmail.com>
Date: Wed, 11 Sep 2024 10:51:27 +0100
Subject: [PATCH] 432 new feature willard chandler density parameter (#433)

* Add density cutoff argument to Willard Chandler
* Delete .travis.yml.  (Invalid file name causes cloning to fail on Windows)

---------

Co-authored-by: Alex Moriarty <25207558+a-ws-m@users.noreply.github.com>
Co-authored-by: a-ws-m <amoriarty14@gmail.com>
---
 .travis.yml.              | 61 ---------------------------------------
 pytim/willard_chandler.py |  7 ++++-
 2 files changed, 6 insertions(+), 62 deletions(-)
 delete mode 100644 .travis.yml.

diff --git a/.travis.yml. b/.travis.yml.
deleted file mode 100644
index 2cd29d8e..00000000
--- a/.travis.yml.
+++ /dev/null
@@ -1,61 +0,0 @@
-language: python
-
-branches:
-  except:
-  - dev
-  - extended_datafiles
-
-
-env:
-    global:
-        - CC_TEST_REPORTER_ID=bdc5010b5f2e62769ccd2d885f0d7eb59691844de9a2018e9e3da255a37282e2
-
-matrix:
-    include:
-
-        - os: linux
-          sudo: required
-          python: 3.6
-          env: MDAv=1.0.0
-
-       # - os: osx
-       #   language: generic
-       #   env: MDAv=0.16
-
-
-before_install:
-    - if [[ "$TRAVIS_OS_NAME" == "osx"   ]] ; then 
-        brew update;
-        curl -s --location "https://bootstrap.pypa.io/get-pip.py" -o get-pip.py ;
-        python get-pip.py --user ; 
-        alias pip='pip2'
-        pip install --upgrade pip  ; 
-      fi
-#    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] ; then sudo apt-get install liblapack-dev -y   ; fi
-
-install:
-- pip install codecov
-- pip install pylama
-- pip install pytest-cov
-- pip install Sphinx>=1.4.3
-- pip install matplotlib
-- pip install cython
-- pip install MDAnalysis==$MDAv
-- pip install pandas
-- pip install mdtraj
-- pip install nose
-- pip install .
-# command to run tests
-
-before_script:
-  - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
-  - chmod +x ./cc-test-reporter
-  - ./cc-test-reporter before-build
-
-script: python setup.py test
-
-
-after_script:
-  if ([ "$TRAVIS_OS_NAME" == "linux" ] && [ "$MDAv" == "0.19" ]) ; then
-        pip install codecov; pip install pytest-cov ; py.test --cov=pytim pytim/*py pytim/observables/*py pytim/datafiles/*py --doctest-modules --cov-report xml ;  ./cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT ; codecov ; fi
-
diff --git a/pytim/willard_chandler.py b/pytim/willard_chandler.py
index 9f433db1..1961dab5 100644
--- a/pytim/willard_chandler.py
+++ b/pytim/willard_chandler.py
@@ -39,6 +39,9 @@ class WillardChandler(Interface):
                                   this group
         :param float alpha:       The width of the Gaussian kernel
         :param float mesh:        The grid spacing for the density calculation
+        :param float density_cutoff: The density value used to define the
+                                  isosurface. `None` (default) uses the average
+                                  of the minimum and maximum density.
         :param AtomGroup group:   Compute the density using this group
         :param dict radii_dict:   Dictionary with the atomic radii of
                                   the elements in the group.
@@ -127,10 +130,12 @@ def __init__(self,
                  centered=False,
                  warnings=False,
                  autoassign=True,
+                 density_cutoff=None,
                  **kargs):
 
         self.autoassign, self.do_center = autoassign, centered
         self.include_zero_radius = include_zero_radius
+        self.density_cutoff = density_cutoff
         sanity = SanityCheck(self, warnings=warnings)
         sanity.assign_universe(universe, group)
         sanity.assign_alpha(alpha)
@@ -245,7 +250,7 @@ def _assign_layers(self):
         volume = self.density_field.reshape(
             tuple(np.array(ngrid[::-1]).astype(int)))
         verts, faces, normals, values = marching_cubes(
-            volume, None, spacing=tuple(spacing))
+            volume, self.density_cutoff, spacing=tuple(spacing))
         # note that len(normals) == len(verts): they are normals
         # at the vertices, and not normals of the faces
         # verts and normals have x and z flipped because skimage uses zyx ordering