Update requirements, minor fixes

* Minor differences in ITIM results due to changes in depedencies
* Version bump

Author: Marcello-Sega

.circleci/config.yml

@@ -21,7 +21,7 @@ jobs:
     # The executor is the environment in which the steps below will be executed - below will use a python 3.8 container
     # Change the version below to your required version of python
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.9
     # Checkout the code as the first step. This is a dedicated CircleCI step.
     # The python orb's install-packages step will install the dependencies from a Pipfile via Pipenv by default.
     # Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
@@ -35,10 +35,10 @@ jobs:
           # pip-dependency-file: test-requirements.txt  # if you have a different name for your requirements file, maybe one that combines your runtime and test requirements.
       - run:
           name: Install pytim
-          command: pip install  -r requirements.txt -r requirements.testing.txt -e .
+          command: pip install --upgrade -r requirements.txt -r requirements.testing.txt -e .
       - run:
           name: Run tests
-          command: python setup.py test
+          command: pytest pytim/*py pytim/observables/*py pytim/datafiles/*py --doctest-modules
           #  - run:
           #name: Coverage
           # # This assumes pytest is installed via the install-package step above

.github/workflows/python-package.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.11"]
+        python-version: ["3.9", "3.11"]
         include:
           - python-version: "3.9"
             numpy-version: "1.26.4"
@@ -31,7 +31,7 @@ jobs:
         python -m pip install flake8 pytest
         python -m pip install mdtraj
         python -m pip install .
-                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+                if [ -f requirements.txt ]; then pip install --upgrade -r requirements.txt; fi
     #- name: Lint with flake8
      # run: |
      #   # stop the build if there are Python syntax errors or undefined names
@@ -40,5 +40,5 @@ jobs:
      #   flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-         pytest pytim/*py pytim/observables/*py pytim/datafiles/*py --doctest-modules
+         pytest pytim/ --doctest-modules
          

pytim/interface.py

@@ -190,7 +190,7 @@ def _define_cluster_group(self):
             labels = np.array(labels)
 
             # counts is not necessarily ordered by size of cluster.
-            sorting = np.argsort(counts)[::-1]
+            sorting = np.argsort(counts,kind='stable')[::-1]
             # labels for atoms in each cluster starting from the largest
             unique_labels = np.sort(np.unique(labels[labels > -1]))
             # by default, all elements of the cluster_group are in

pytim/itim.py

@@ -85,15 +85,15 @@ class ITIM(Interface):
         >>> print (interface.layers)
         [[<AtomGroup with 786 atoms> <AtomGroup with 681 atoms>
           <AtomGroup with 663 atoms> <AtomGroup with 651 atoms>]
-         [<AtomGroup with 786 atoms> <AtomGroup with 702 atoms>
-          <AtomGroup with 666 atoms> <AtomGroup with 636 atoms>]]
+         [<AtomGroup with 786 atoms> <AtomGroup with 699 atoms>
+          <AtomGroup with 669 atoms> <AtomGroup with 636 atoms>]]
 
 
         >>> interface.layers[0,0] # upper side, first layer
         <AtomGroup with 786 atoms>
 
         >>> interface.layers[1,2] # lower side, third layer
-        <AtomGroup with 666 atoms>
+        <AtomGroup with 669 atoms>
 
         >>> # or as a whole AtomGroup. This can include all atoms in all layers
         >>> interface.atoms
@@ -170,12 +170,12 @@ def layers(self):
         >>> print(interface.layers[:,0:3]) # 1st - 3rd layer (0:3), on both sides
         [[<AtomGroup with 786 atoms> <AtomGroup with 681 atoms>
           <AtomGroup with 663 atoms>]
-         [<AtomGroup with 786 atoms> <AtomGroup with 702 atoms>
-          <AtomGroup with 666 atoms>]]
+         [<AtomGroup with 786 atoms> <AtomGroup with 699 atoms>
+          <AtomGroup with 669 atoms>]]
 
 
         >>> print(interface.layers[1,0:4:2]) # side 1, layers 1-4 & stride 2 (0:4:2)
-        [<AtomGroup with 786 atoms> <AtomGroup with 666 atoms>]
+        [<AtomGroup with 786 atoms> <AtomGroup with 669 atoms>]
 
         """
 
@@ -380,7 +380,7 @@ def _assign_layers(self):
         _y = utilities.get_y(self.cluster_group, self.normal)
         _z = utilities.get_z(self.cluster_group, self.normal)
 
-        sort = np.argsort(_z + _radius * np.sign(_z))
+        sort = np.argsort(_z + _radius * np.sign(_z),kind='stable')
         # NOTE: np.argsort returns the sorted *indices*
 
         if self.multiproc and ('win' not in self.system.lower()):

pytim/observables/contactangle.py

@@ -496,7 +496,7 @@ def _fit_ellipse_fitzgibbon(x, y):
         C = np.zeros((6, 6), dtype=float)
         C[0, 2], C[2, 0], C[1, 1] = 2, 2, -1
         eigval, eigvec = np.linalg.eig(np.linalg.solve(S, C))
-        sort = np.argsort(eigval)
+        sort = np.argsort(eigval,kind='stable')
         eigval, eigvec = eigval[sort], eigvec[sort]
         lam = np.nonzero(np.logical_and(
             eigval > 0, np.isfinite(eigval)))[0][-1]
@@ -515,7 +515,7 @@ def _fit_ellipse_flusser(x, y):
         C = np.array(((0, 0, 2), (0, -1, 0), (2, 0, 0)), dtype=float)
         M = np.linalg.solve(C, M)
         eigval, eigvec = np.linalg.eig(M)
-        sort = np.argsort(eigval)[::-1]
+        sort = np.argsort(eigval,kind='stable')[::-1]
         eigval, eigvec = eigval[sort], eigvec[sort]
         con = 4 * eigvec[0] * eigvec[2] - eigvec[1]**2 > 0
         ak = eigvec[:, np.nonzero(con)[0]]

pytim/utilities.py

@@ -72,17 +72,15 @@ def correlate(a1, a2=None, _normalize=True):
       ...     size.append(len(inter.layers[0,0]))
       >>>
       >>> # we need to subtract the average value
-      >>> np.set_printoptions(precision=3,threshold=1000)
+      >>> np.set_printoptions(precision=3,threshold=1000,suppress=True)
       >>> corr = pytim.utilities.correlate(size-np.mean(size))
       >>> corr = corr/corr[0] # normalize to 1
       >>> print (corr)
-      [ 1.     0.142  0.104  0.147  0.371  0.099  0.165  0.095  0.338  0.219
-       -0.021  0.087  0.245 -0.01  -0.193  0.103  0.029 -0.009 -0.11   0.012
-       -0.133  0.056 -0.283 -0.276  0.035 -0.012 -0.211 -0.429 -0.132 -0.263
-        0.072 -0.7   -0.236  0.136 -0.243 -0.878 -0.13  -0.329 -0.386 -0.652
-       -0.267 -0.188 -0.226 -0.79  -0.284 -0.02  -1.512 -1.316 -0.188  7.551]
-
-      >>> np.set_printoptions()
+      [ 1.     0.153  0.104  0.17   0.365  0.115  0.171  0.104  0.342  0.24
+       -0.021  0.097  0.265  0.004 -0.169  0.088  0.022 -0.008 -0.113  0.003
+       -0.139  0.051 -0.287 -0.279  0.027 -0.019 -0.223 -0.43  -0.157 -0.285
+        0.048 -0.704 -0.26   0.13  -0.31  -0.883 -0.12  -0.323 -0.388 -0.64
+       -0.295 -0.177 -0.165 -0.81  -0.321 -0.031 -1.557 -1.296 -0.305  6.974]
 
       This will produce (sampling the whole trajectory), the following:
 

pytim/version.py

@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = '1.0.1'

requirements.txt

@@ -1,8 +1,8 @@
 cython>=0.24.1
-numpy>=1.16.0
+numpy>=1.26.4,<2.0.0
 scipy>=1.6.0
-gsd<=3.2.1
-MDAnalysis>=2.0
+gsd>3.0.0
+MDAnalysis>=2.7.0
 PyWavelets>=0.5.2
 scikit-image>=0.14.2
 sphinx>=1.4.3 

setup.py

@@ -125,7 +125,7 @@ def run_tests(self):
     # requirements files see:
     # https://packaging.python.org/en/latest/requirements.html
     install_requires=[
-        'numpy>=1.16', 'cython>=0.24.1','gsd<=3.2.1'
+        'numpy>=1.26.4,<2.0.0', 'cython>=0.24.1','gsd>=3.0.0','MDAnalysis>=2.7.0'
     ],
 
     # List additional groups of dependencies here (e.g. development