Merge pull request #76 from dwhswenson/release-0.5.1

Release 0.5.1

.travis.yml

@@ -2,8 +2,8 @@ version: ~> 1.0
 
 language: python
 python:
+  - '3.8'
   - '3.7'
-  - '2.7'
   - '3.6'
 
 notifications:
@@ -17,22 +17,24 @@ branches:
 
 env:
   global:
-    - CANONICAL_PYTHON="3.7"
+    - CANONICAL_PYTHON="3.8"
     - CANONICAL_MDTRAJ="release"
     - CODECLIMATE=""
     - TWINE_USERNAME="dwhswenson"
     # TWINE_PASSWORD
     - secure: "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"
     # AUTORELEASE_TOKEN
     - secure: "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"
-  matrix:
+  jobs:
     - MDTRAJ="release"
     - MDTRAJ="dev"
 
 jobs:
   exclude:
     - env: MDTRAJ="dev"
       python: "3.6"
+    - env: MDTRAJ="dev"
+      python: "3.7"
 
 before_install:
   - echo "before install"
@@ -58,7 +60,6 @@ after_success:
   - coveralls
   - python-codacy-coverage -r cov.xml
 
-
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.0
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.2.1
 

appveyor.yml

@@ -14,26 +14,24 @@ environment:
     PYTHONUNBUFFERED: 1
 
   matrix:
-    - PYTHON: "C:\\Miniconda"
-      CONDA_PY: "27"
-      ARCH: '32'
-    - PYTHON: "C:\\Miniconda-x64"
-      CONDA_PY: "27"
-      ARCH: '64'
-    - PYTHON: "C:\\Miniconda36"
-      CONDA_PY: "36" # No MDTraj for py37/Win32
-      ARCH: '32'
+    #- PYTHON: "C:\\Miniconda38-x64"
+      #CONDA_PY: "38" 
+      #ARCH: '64'
     - PYTHON: "C:\\Miniconda37-x64"
       CONDA_PY: "37"
       ARCH: '64'
+    - PYTHON: "C:\\Miniconda36-x64"
+      CONDA_PY: "36" 
+      ARCH: '64'
 
 build: false
 
 install:
-  # install python
+  # set up conda Python
   - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%
   - conda config --add channels conda-forge
-  - conda install -yq conda=4.5 conda-build=3.10
+  # note: it may become necessary to pin versions of conda/conda-build
+  - conda install -yq conda conda-build
 
 test_script:
   #- "%CMD_IN_ENV% activate base"

ci/conda-recipe/meta.yaml

@@ -1,7 +1,7 @@
 package:
   name: contact_map
   # add ".dev0" for unreleased versions
-  version: "0.5.0"
+  version: "0.5.1"
 
 source:
   path: ../../
@@ -20,7 +20,7 @@ requirements:
     - mdtraj
     - numpy
     - scipy
-    - pandas<1.0
+    - pandas
 
 test:
   requires:

contact_map/contact_count.py

@@ -13,6 +13,8 @@
 else:
     HAS_MATPLOTLIB = True
 
+# pandas 0.25 not available on py27; can drop this when we drop py27
+_PD_VERSION = tuple(int(x) for x in pd.__version__.split('.')[:2])
 
 def _colorbar(with_colorbar, cmap_f, norm, min_val):
     if with_colorbar is False:
@@ -25,6 +27,34 @@ def _colorbar(with_colorbar, cmap_f, norm, min_val):
     return cb
 
 
+# TODO: remove following: this is a monkeypatch for a bug in pandas
+# see: https://github.com/pandas-dev/pandas/issues/29814
+from pandas._libs.sparse import BlockIndex, IntIndex, SparseIndex
+def _patch_from_spmatrix(cls, data):
+    length, ncol = data.shape
+
+    if ncol != 1:
+        raise ValueError("'data' must have a single column, not '{}'".format(ncol))
+
+    # our sparse index classes require that the positions be strictly
+    # increasing. So we need to sort loc, and arr accordingly.
+    arr = data.data
+    #idx, _ = data.nonzero()
+    idx = data.indices
+    loc = np.argsort(idx)
+    arr = arr.take(loc)
+    idx.sort()
+
+    zero = np.array(0, dtype=arr.dtype).item()
+    dtype = pd.SparseDtype(arr.dtype, zero)
+    index = IntIndex(length, idx)
+
+    return cls._simple_new(arr, index, dtype)
+
+if _PD_VERSION >= (0, 25):
+    pd.core.arrays.SparseArray.from_spmatrix = classmethod(_patch_from_spmatrix)
+# TODO: this is the end of what to remove when pandas is fixed
+
 class ContactCount(object):
     """Return object when dealing with contacts (residue or atom).
 
@@ -95,10 +125,22 @@ def df(self):
             Rows/columns correspond to indices and the values correspond to
             the count
         """
-        mtx = self.sparse_matrix.tocoo()
+        mtx = self.sparse_matrix
         index = list(range(self.n_x))
         columns = list(range(self.n_y))
-        return pd.SparseDataFrame(mtx, index=index, columns=columns)
+
+        if _PD_VERSION < (0, 25):  # py27 only
+            mtx = mtx.tocoo()
+            return pd.SparseDataFrame(mtx, index=index, columns=columns)
+
+        df = pd.DataFrame.sparse.from_spmatrix(mtx, index=index,
+                                               columns=columns)
+        # note: I think we can always use float here for dtype; but in
+        # principle maybe we need to inspect and get the internal type?
+        # Problem is, pandas technically stores a different dtype for each
+        # column.
+        df = df.astype(pd.SparseDtype("float", np.nan))
+        return df
 
     def _check_number_of_pixels(self, figure):
         """

contact_map/tests/test_contact_count.py

@@ -89,12 +89,23 @@ def test_sparse_matrix(self):
     def test_df(self):
         atom_df = self.map.atom_contacts.df
         residue_df = self.map.residue_contacts.df
-        assert isinstance(atom_df, pd.SparseDataFrame)
-        assert isinstance(residue_df, pd.SparseDataFrame)
 
-        assert_array_equal(atom_df.to_dense().values,
+        # this block is for old pandas on py27
+        pd_version = tuple(int(x) for x in pd.__version__.split('.')[:2])
+        if pd_version < (0, 25):
+            assert isinstance(atom_df, pd.SparseDataFrame)
+            assert isinstance(residue_df, pd.SparseDataFrame)
+            assert_array_equal(atom_df.to_dense().values,
+                               zero_to_nan(self.atom_matrix))
+            assert_array_equal(residue_df.to_dense().values,
+                               zero_to_nan(self.residue_matrix))
+            return
+
+        assert isinstance(atom_df, pd.DataFrame)
+        assert isinstance(residue_df, pd.DataFrame)
+        assert_array_equal(atom_df.sparse.to_dense().values,
                            zero_to_nan(self.atom_matrix))
-        assert_array_equal(residue_df.to_dense().values,
+        assert_array_equal(residue_df.sparse.to_dense().values,
                            zero_to_nan(self.residue_matrix))
 
     @pytest.mark.parametrize("obj_type", ['atom', 'res'])

docs/conf.py

@@ -101,7 +101,7 @@
 
 # General information about the project.
 project = u'Contact Map Explorer'
-copyright = u'2017-2019, David W.H. Swenson and Sander Roet'
+copyright = u'2017-2020, David W.H. Swenson and Sander Roet'
 author = u'David W.H. Swenson and Sander Roet'
 
 # The language for content autogenerated by Sphinx. Refer to documentation

readthedocs.yml

@@ -1,13 +1,13 @@
 version: 2
 
-conda:
-    environment: docs/environment.yml
+#conda:
+    #environment: docs/environment.yml
 
 python:
     install:
-      #- requirements: docs/rtd_requirements.txt
+      - requirements: docs/rtd_requirements.txt
       #- requirements: requirements.txt
-      #- requirements: docs/requirements.txt
+      - requirements: docs/requirements.txt
       - method: setuptools
         path: .
       #- method: pip

requirements.txt

@@ -1,5 +1,5 @@
 future
 numpy
 scipy
-pandas<1.0
+pandas
 mdtraj

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = contact_map
-version = 0.5.0
+version = 0.5.1
 description = Contact maps based on MDTraj
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -26,7 +26,7 @@ install_requires =
     numpy
     mdtraj
     scipy
-    pandas<1.0
+    pandas
 packages = find:
 
 [bdist_wheel]