From 53c0b481b73fc7051b3bc667ec237d49fc6e1f28 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Sat, 8 Feb 2020 13:01:28 +0100
Subject: [PATCH 01/21] Fixes for sparse matrix in Pandas 1.0

For now, there seems to be a bug in pandas; so we may need to
wait on that. I think (still need to confirm) that this is the
source of the test failures.
---
 contact_map/contact_count.py            | 13 +++++++++++--
 contact_map/tests/test_contact_count.py |  8 ++++----
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/contact_map/contact_count.py b/contact_map/contact_count.py
index c9beb2e..550e076 100644
--- a/contact_map/contact_count.py
+++ b/contact_map/contact_count.py
@@ -95,10 +95,19 @@ def df(self):
             Rows/columns correspond to indices and the values correspond to
             the count
         """
-        mtx = self.sparse_matrix.tocoo()
+        # 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)
+        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 pd.SparseDataFrame(mtx, index=index, columns=columns)
+        return df
 
     def _check_number_of_pixels(self, figure):
         """
diff --git a/contact_map/tests/test_contact_count.py b/contact_map/tests/test_contact_count.py
index ef91eb3..c85a14a 100644
--- a/contact_map/tests/test_contact_count.py
+++ b/contact_map/tests/test_contact_count.py
@@ -89,12 +89,12 @@ 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 isinstance(atom_df, pd.DataFrame)
+        assert isinstance(residue_df, pd.DataFrame)
 
-        assert_array_equal(atom_df.to_dense().values,
+        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'])

From 9b3ada89aa536e2afaa9c88a8adb4baa9e808be7 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Wed, 12 Feb 2020 12:44:25 +0100
Subject: [PATCH 02/21] Bump version on master to 0.5.1.dev0

---
 ci/conda-recipe/meta.yaml | 2 +-
 setup.cfg                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/conda-recipe/meta.yaml b/ci/conda-recipe/meta.yaml
index 8ea4c9d..3f74281 100644
--- a/ci/conda-recipe/meta.yaml
+++ b/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.dev0"
 
 source:
   path: ../../
diff --git a/setup.cfg b/setup.cfg
index d6415dd..199836f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = contact_map
-version = 0.5.0
+version = 0.5.1.dev0
 description = Contact maps based on MDTraj
 long_description = file: README.md
 long_description_content_type = text/markdown

From 144a0ab0fe1e4035d255dae46a05fad14e15ea93 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Thu, 13 Feb 2020 15:10:12 +0100
Subject: [PATCH 03/21] monkey patch for pandas sparse bug

---
 ci/conda-recipe/meta.yaml    |  2 +-
 contact_map/contact_count.py | 27 +++++++++++++++++++++++++++
 requirements.txt             |  2 +-
 setup.cfg                    |  2 +-
 4 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/ci/conda-recipe/meta.yaml b/ci/conda-recipe/meta.yaml
index 3f74281..bdc6572 100644
--- a/ci/conda-recipe/meta.yaml
+++ b/ci/conda-recipe/meta.yaml
@@ -20,7 +20,7 @@ requirements:
     - mdtraj
     - numpy
     - scipy
-    - pandas<1.0
+    - pandas
 
 test:
   requires:
diff --git a/contact_map/contact_count.py b/contact_map/contact_count.py
index 550e076..033c7b3 100644
--- a/contact_map/contact_count.py
+++ b/contact_map/contact_count.py
@@ -25,6 +25,33 @@ 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)
+
+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).
 
diff --git a/requirements.txt b/requirements.txt
index 2bc28c8..6cd0d95 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 future
 numpy
 scipy
-pandas<1.0
+pandas
 mdtraj
diff --git a/setup.cfg b/setup.cfg
index 199836f..63f45c5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,7 +26,7 @@ install_requires =
     numpy
     mdtraj
     scipy
-    pandas<1.0
+    pandas
 packages = find:
 
 [bdist_wheel]

From 5b63aefdaabc57722150956c73ca70fbc79dd6e7 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Thu, 13 Feb 2020 15:40:15 +0100
Subject: [PATCH 04/21] only monkey patch later versions of pandas

---
 contact_map/contact_count.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/contact_map/contact_count.py b/contact_map/contact_count.py
index 033c7b3..a822328 100644
--- a/contact_map/contact_count.py
+++ b/contact_map/contact_count.py
@@ -49,7 +49,9 @@ def _patch_from_spmatrix(cls, data):
 
     return cls._simple_new(arr, index, dtype)
 
-pd.core.arrays.SparseArray.from_spmatrix = classmethod(_patch_from_spmatrix)
+_PD_VERSION = tuple(int(x) for x in pd.__version__.split('.')[:2])
+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):

From 0d3458d8236ec6efb44a8beba017b8fc12d6d99d Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Thu, 13 Feb 2020 16:01:46 +0100
Subject: [PATCH 05/21] more py27 alternate implementations

---
 contact_map/contact_count.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/contact_map/contact_count.py b/contact_map/contact_count.py
index a822328..4e57732 100644
--- a/contact_map/contact_count.py
+++ b/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:
@@ -49,7 +51,6 @@ def _patch_from_spmatrix(cls, data):
 
     return cls._simple_new(arr, index, dtype)
 
-_PD_VERSION = tuple(int(x) for x in pd.__version__.split('.')[:2])
 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
@@ -124,10 +125,14 @@ 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))
+
+        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
@@ -135,7 +140,6 @@ def df(self):
         # Problem is, pandas technically stores a different dtype for each
         # column.
         df = df.astype(pd.SparseDtype("float", np.nan))
-        # return pd.SparseDataFrame(mtx, index=index, columns=columns)
         return df
 
     def _check_number_of_pixels(self, figure):

From 8ad7aa2132522d85a4fd51e14b076cee7f713d6b Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Thu, 13 Feb 2020 16:09:33 +0100
Subject: [PATCH 06/21] add testing path for py27

---
 contact_map/tests/test_contact_count.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/contact_map/tests/test_contact_count.py b/contact_map/tests/test_contact_count.py
index c85a14a..77f3a5d 100644
--- a/contact_map/tests/test_contact_count.py
+++ b/contact_map/tests/test_contact_count.py
@@ -89,9 +89,20 @@ def test_sparse_matrix(self):
     def test_df(self):
         atom_df = self.map.atom_contacts.df
         residue_df = self.map.residue_contacts.df
+
+        # 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.sparse.to_dense().values,

From 4b040aa522c22307120a011c14f5628069a37a3b Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Fri, 14 Feb 2020 11:44:02 +0100
Subject: [PATCH 07/21] try to switch to setuptools-based RTD install

---
 readthedocs.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/readthedocs.yml b/readthedocs.yml
index dfbea26..c17a8f1 100644
--- a/readthedocs.yml
+++ b/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

From 06815abcd3218fa371eb602d127dfa8ef9d6da74 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Fri, 14 Feb 2020 11:55:06 +0100
Subject: [PATCH 08/21] bump copyright year

---
 docs/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index 0edcb3c..89cddec 100644
--- a/docs/conf.py
+++ b/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

From 8419ef804a40b34659a2308ca2d9478865d84bd8 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 30 Jun 2020 11:06:08 +0200
Subject: [PATCH 09/21] Test matrix: Drop Py27 and Win32; add Py38

---
 .travis.yml  |  6 ++++--
 appveyor.yml | 13 +++++--------
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index e9ba691..0fab42e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,8 +2,8 @@ version: ~> 1.0
 
 language: python
 python:
+  - '3.8'
   - '3.7'
-  - '2.7'
   - '3.6'
 
 notifications:
@@ -17,7 +17,7 @@ branches:
 
 env:
   global:
-    - CANONICAL_PYTHON="3.7"
+    - CANONICAL_PYTHON="3.8"
     - CANONICAL_MDTRAJ="release"
     - CODECLIMATE=""
     - TWINE_USERNAME="dwhswenson"
@@ -33,6 +33,8 @@ jobs:
   exclude:
     - env: MDTRAJ="dev"
       python: "3.6"
+    - env: MDTRAJ="dev"
+      python: "3.7"
 
 before_install:
   - echo "before install"
diff --git a/appveyor.yml b/appveyor.yml
index d2eda24..1f239b6 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -14,18 +14,15 @@ environment:
     PYTHONUNBUFFERED: 1
 
   matrix:
-    - PYTHON: "C:\\Miniconda"
-      CONDA_PY: "27"
-      ARCH: '32'
-    - PYTHON: "C:\\Miniconda-x64"
-      CONDA_PY: "27"
+    - PYTHON: "C:\\Miniconda38-x64"
+      CONDA_PY: "38" 
       ARCH: '64'
-    - PYTHON: "C:\\Miniconda36"
-      CONDA_PY: "36" # No MDTraj for py37/Win32
-      ARCH: '32'
     - PYTHON: "C:\\Miniconda37-x64"
       CONDA_PY: "37"
       ARCH: '64'
+    - PYTHON: "C:\\Miniconda36-x64"
+      CONDA_PY: "36" 
+      ARCH: '64'
 
 build: false
 

From 7088d1d40ba7badee953d587e4a9aba73ab2a528 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 30 Jun 2020 11:41:33 +0200
Subject: [PATCH 10/21] use most recent conda / conda-build in AppVeyor

---
 appveyor.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 1f239b6..34d4509 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -30,7 +30,8 @@ install:
   # install python
   - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%
   - conda config --add channels conda-forge
-  - conda install -yq conda=4.5 conda-build=3.10
+  #- conda install -yq conda=4.5 conda-build=3.10
+  - conda install -yq conda conda-build
 
 test_script:
   #- "%CMD_IN_ENV% activate base"

From f8a1609b643422f3696b16050707b18cf60673f0 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 30 Jun 2020 12:10:05 +0200
Subject: [PATCH 11/21] try adding condabin dir for AppVeyor

---
 appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 34d4509..8e03106 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -28,7 +28,7 @@ build: false
 
 install:
   # install python
-  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%
+  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON\\condabin;%PATH%
   - conda config --add channels conda-forge
   #- conda install -yq conda=4.5 conda-build=3.10
   - conda install -yq conda conda-build

From 5547039c2f799e70dd5de05c744b34747dc80cff Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 30 Jun 2020 12:28:44 +0200
Subject: [PATCH 12/21] Another attempt with AppVeyor

---
 appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 8e03106..79ea3d9 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -28,7 +28,7 @@ build: false
 
 install:
   # install python
-  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON\\condabin;%PATH%
+  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON\\bin;%PATH\\Library\\bin;%PATH%
   - conda config --add channels conda-forge
   #- conda install -yq conda=4.5 conda-build=3.10
   - conda install -yq conda conda-build

From 652a41c60ccffd0f2148556e6dbf6bbc4a1c43b4 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 30 Jun 2020 12:37:28 +0200
Subject: [PATCH 13/21] AppVeyor

---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index 79ea3d9..0a778b7 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -29,6 +29,7 @@ build: false
 install:
   # install python
   - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON\\bin;%PATH\\Library\\bin;%PATH%
+  - call %PYTHON%\Scripts\activate.bat
   - conda config --add channels conda-forge
   #- conda install -yq conda=4.5 conda-build=3.10
   - conda install -yq conda conda-build

From 64ff50b019d55111b72dff0672f0a0522f673088 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Tue, 30 Jun 2020 12:48:30 +0200
Subject: [PATCH 14/21] Disable AppVeyor/Python38 (no one else using?)

---
 appveyor.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 0a778b7..da6d8e0 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -14,9 +14,9 @@ environment:
     PYTHONUNBUFFERED: 1
 
   matrix:
-    - PYTHON: "C:\\Miniconda38-x64"
-      CONDA_PY: "38" 
-      ARCH: '64'
+    #- PYTHON: "C:\\Miniconda38-x64"
+      #CONDA_PY: "38" 
+      #ARCH: '64'
     - PYTHON: "C:\\Miniconda37-x64"
       CONDA_PY: "37"
       ARCH: '64'
@@ -29,7 +29,6 @@ build: false
 install:
   # install python
   - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON\\bin;%PATH\\Library\\bin;%PATH%
-  - call %PYTHON%\Scripts\activate.bat
   - conda config --add channels conda-forge
   #- conda install -yq conda=4.5 conda-build=3.10
   - conda install -yq conda conda-build

From a8b12ac27a9abcd618db61b8b28379bafc802978 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Thu, 2 Jul 2020 13:08:55 +0200
Subject: [PATCH 15/21] updates for Sander's review

---
 .travis.yml  | 7 ++-----
 appveyor.yml | 6 +++---
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0fab42e..5e42d84 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -27,14 +27,11 @@ env:
     - secure: "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"
   matrix:
     - MDTRAJ="release"
-    - MDTRAJ="dev"
 
 jobs:
-  exclude:
+  include:
     - env: MDTRAJ="dev"
-      python: "3.6"
-    - env: MDTRAJ="dev"
-      python: "3.7"
+      python: "3.8"
 
 before_install:
   - echo "before install"
diff --git a/appveyor.yml b/appveyor.yml
index da6d8e0..9513a21 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -27,10 +27,10 @@ environment:
 build: false
 
 install:
-  # install python
-  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON\\bin;%PATH\\Library\\bin;%PATH%
+  # 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:

From 71a22613146f308f5492249743055d764cee7404 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Thu, 2 Jul 2020 13:56:44 +0200
Subject: [PATCH 16/21] Switch travis back to excludes

---
 .travis.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 5e42d84..f600e90 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,13 +25,16 @@ env:
     - secure: "onsUSX6Yxt0HJApAsyUr5iFQW1ZngBiMxKmdiI5aN0TqnVSQ6819xx0YIxBjgburG/pFoW1F8bh8KYITV6TKK7RpcwdOspqpeO0X6L0DdBvNWQdl99QtJZcuMS3nPBiJ4guwrJCkQa/iKgZ7k27YukTw5pgKKDgC2d10P5SQiVFHNkX8lo4FzZIBnpA93Nq9G+j2pi14PpGtxaXhktqLOSvLvy/7BIWfzy69HDGjKZ38SMF4RFRnHiBI0G2uON6N5AuLovBWpRrmPmCTiX3p2lgxss8oUSKsA9OlikAoGlLyOjzMU2Fu3JqgoXPSyjDzkqO/Bavd1S03RYUeB5cRM9kBoORjCYl2dBCAmh7U41ZigvivYC2UZ/2p300f9YmolZ4vcj9tz4THXfF5/ZgIoARFIVk3fIQOHJCnXwa3gDcf0AEmsYOUOSKJKyYxruQhyjb2reFxUyA6bqtelV82qpMT53fSZ1/ZJjA+yJJgbeB9qkrMjvUf9AjlY8faqXyIafJsogFuvg1rg+FddMlc56zUWCEdc/pgbTesQuF8GCqje++7eaN68KiWBPwjDSX6cuNkeg86xx1E4VsRcXH6rQ9JXCsGs/HN4JRZ5J+ZH4YOHaUc5pTG82mTEZHGCjAN+BuhGfSFcgSoGO6oOHRGVjw47emOLvNpjS05B/zu/4c="
     # AUTORELEASE_TOKEN
     - secure: "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"
-  matrix:
+  jobs:
     - MDTRAJ="release"
+    - MDTRAJ="dev"
 
 jobs:
-  include:
+  exclude:
     - env: MDTRAJ="dev"
-      python: "3.8"
+      python: "3.6"
+    - env: MDTRAJ="dev"
+      python: "3.7"
 
 before_install:
   - echo "before install"

From e5f023a5e77eac16192c51441a3c98fe094f8f80 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Wed, 8 Jul 2020 14:14:57 +0200
Subject: [PATCH 17/21] Release 0.5.1

---
 ci/conda-recipe/meta.yaml | 2 +-
 setup.cfg                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/conda-recipe/meta.yaml b/ci/conda-recipe/meta.yaml
index bdc6572..e5734db 100644
--- a/ci/conda-recipe/meta.yaml
+++ b/ci/conda-recipe/meta.yaml
@@ -1,7 +1,7 @@
 package:
   name: contact_map
   # add ".dev0" for unreleased versions
-  version: "0.5.1.dev0"
+  version: "0.5.1"
 
 source:
   path: ../../
diff --git a/setup.cfg b/setup.cfg
index 63f45c5..dfaa6e6 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = contact_map
-version = 0.5.1.dev0
+version = 0.5.1
 description = Contact maps based on MDTraj
 long_description = file: README.md
 long_description_content_type = text/markdown

From b55e9e39b8c3ea9bff8122b92a4c753ab071c306 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Wed, 8 Jul 2020 14:36:20 +0200
Subject: [PATCH 18/21] Try autorelease experimental stage ordering

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index f600e90..57ea6c9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -62,5 +62,5 @@ after_success:
 
 
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.0
+  - dwhswenson/autorelease:autorelease-travis.yml@stage_order
 

From 3e69fd84c7437ddbb279d02da07aec6f47571d2b Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Wed, 8 Jul 2020 15:11:54 +0200
Subject: [PATCH 19/21] try stages in main travis?

---
 .travis.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 57ea6c9..0034c8f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -60,6 +60,12 @@ after_success:
   - coveralls
   - python-codacy-coverage -r cov.xml
 
+stages:
+    - test
+    - deploy_testpypi
+    - test_testpypi
+    - deploy_pypi
+    - cut_release
 
 import:
   - dwhswenson/autorelease:autorelease-travis.yml@stage_order

From 58dd4e6da2b75cb1d5f393863b39c0a18f9856d6 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Wed, 8 Jul 2020 15:51:34 +0200
Subject: [PATCH 20/21] remove stages from .travis.yml

---
 .travis.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0034c8f..a3fa441 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -60,13 +60,6 @@ after_success:
   - coveralls
   - python-codacy-coverage -r cov.xml
 
-stages:
-    - test
-    - deploy_testpypi
-    - test_testpypi
-    - deploy_pypi
-    - cut_release
-
 import:
   - dwhswenson/autorelease:autorelease-travis.yml@stage_order
 

From 3545755f278a0e8c1b8f163b13ebba4d6e3a4913 Mon Sep 17 00:00:00 2001
From: "David W.H. Swenson" <dwhs@hyperblazer.net>
Date: Wed, 12 Aug 2020 08:14:55 +0200
Subject: [PATCH 21/21] Bump autorelease to 0.2.1 (fix stage ordering)

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a3fa441..09680f5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -61,5 +61,5 @@ after_success:
   - python-codacy-coverage -r cov.xml
 
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@stage_order
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.2.1