Drop support for legacy Python 2.7

.travis.yml

@@ -8,8 +8,6 @@ language: python
 
 matrix:
   include:
-    - os: linux
-      python: 2.7
     - os: linux
       python: 3.6
     - os: osx
@@ -21,8 +19,6 @@ install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
       curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > miniconda.sh;
       export TRAVIS_PYTHON_VERSION="3.6";
-    elif [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
     else
       wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
     fi

docs/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    = -W
-SPHINXBUILD   = sphinx-build
+SPHINXBUILD   = python3 -m sphinx
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/conf.py

@@ -43,7 +43,7 @@ def __getattr__(cls, name):
 # -- Project information -----------------------------------------------------
 
 project = 'tskit'
-copyright = '2018, Tskit developers'
+copyright = '2018-2019, Tskit developers'
 author = 'Tskit developers'
 
 # The short X.Y version
@@ -76,7 +76,7 @@ def handle_item(fieldarg, content):
             # inconsistencies later when references are resolved
             fieldtype = types.pop(fieldarg)
             if len(fieldtype) == 1 and isinstance(fieldtype[0], nodes.Text):
-                typename = u''.join(n.astext() for n in fieldtype)
+                typename = ''.join(n.astext() for n in fieldtype)
                 par.extend(self.make_xrefs(self.typerolename, domain, typename,
                                            addnodes.literal_emphasis))
             else:
@@ -117,8 +117,12 @@ def handle_item(fieldarg, content):
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
     'breathe',
+    'sphinx_issues',
 ]
 
+# Github repo
+issues_github_path = "tskit-dev/tskit"
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/development.rst

@@ -25,8 +25,7 @@ Quickstart
 
 - Install the Python development requirements using
   ``pip install -r python/requirements/development.txt``.
-- Build the low level module by running ``make`` in the ``python`` directory. Python 3.x
-  is the default for developement (Python 2.x is discouraged).
+- Build the low level module by running ``make`` in the ``python`` directory.
 - Run the tests to ensure everything has worked: ``python -m nose -vs``. These should
   all pass.
 - Make your changes in a local branch, and open a pull request on GitHub when you

docs/rtd_requirements.txt

@@ -1,6 +1,6 @@
 numpy
-six
 svgwrite
 jsonschema
 h5py
 breathe
+sphinx-issues

python/CHANGELOG.rst

@@ -1,3 +1,15 @@
+--------------------
+[0.1.5] - 2019-XX-XX
+--------------------
+
+Under development.
+
+This release removes support for Python 2.
+
+**New features**
+
+- Remove support for Python 2 (:user:`hugovk`). See :issue:`137` and :pr:`140`.
+
 --------------------
 [0.1.4] - 2019-02-01
 --------------------

python/Makefile

@@ -8,9 +8,6 @@ allchecks: _tskitmodule.c
 ext3: _tskitmodule.c 
 	python3 setup.py build_ext --inplace
 
-ext2: _tskitmodule.c 
-	python2 setup.py build_ext --inplace
-
 ctags:
 	ctags lib/*.c lib/*.h tskit/*.py
 

python/_tskitmodule.c

@@ -1,21 +1,27 @@
 /*
-** Copyright (C) 2014-2018 University of Oxford
-**
-** This file is part of tskit.
-**
-** tskit is free software: you can redistribute it and/or modify
-** it under the terms of the GNU General Public License as published by
-** the Free Software Foundation, either version 3 of the License, or
-** (at your option) any later version.
-**
-** tskit is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with tskit.  If not, see <http://www.gnu.org/licenses/>.
-*/
+ * MIT License
+ *
+ * Copyright (c) 2019 Tskit Developers
+ * Copyright (c) 2015-2018 University of Oxford
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
 
 #define PY_SSIZE_T_CLEAN
 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
@@ -28,13 +34,6 @@
 #include "kastore.h"
 #include "tskit.h"
 
-#if PY_MAJOR_VERSION >= 3
-#define IS_PY3K
-#endif
-
-#define MODULE_DOC \
-"Low level interface for tskit"
-
 #define SET_COLS 0
 #define APPEND_COLS 1
 
@@ -8427,8 +8426,6 @@ static PyTypeObject LdCalculatorType = {
 static PyObject *
 tskit_get_kastore_version(PyObject *self)
 {
-    /* TODO if we provide the option of linking against kastore separately, we
-     * should return the link time version using kas_get_version */
     return Py_BuildValue("iii", KAS_VERSION_MAJOR, KAS_VERSION_MINOR, KAS_VERSION_PATCH);
 }
 
@@ -8446,49 +8443,28 @@ static PyMethodDef tskit_methods[] = {
     {NULL}        /* Sentinel */
 };
 
-/* Initialisation code supports Python 2.x and 3.x. The framework uses the
- * recommended structure from http://docs.python.org/howto/cporting.html.
- * I've ignored the point about storing state in globals, as the examples
- * from the Python documentation still use this idiom.
- */
-
-#if PY_MAJOR_VERSION >= 3
-
 static struct PyModuleDef tskitmodule = {
     PyModuleDef_HEAD_INIT,
-    "_tskit",   /* name of module */
-    MODULE_DOC, /* module documentation, may be NULL */
+    "_tskit",
+    "Low level interface for tskit",
     -1,
     tskit_methods,
     NULL, NULL, NULL, NULL
 };
 
-#define INITERROR return NULL
-
 PyObject *
 PyInit__tskit(void)
-
-#else
-#define INITERROR return
-
-void
-init_tskit(void)
-#endif
 {
-#if PY_MAJOR_VERSION >= 3
     PyObject *module = PyModule_Create(&tskitmodule);
-#else
-    PyObject *module = Py_InitModule3("_tskit", tskit_methods, MODULE_DOC);
-#endif
     if (module == NULL) {
-        INITERROR;
+        return NULL;
     }
     import_array();
 
     /* LightweightTableCollection type */
     LightweightTableCollectionType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&LightweightTableCollectionType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&LightweightTableCollectionType);
     PyModule_AddObject(module, "LightweightTableCollection",
@@ -8497,111 +8473,111 @@ init_tskit(void)
     /* IndividualTable type */
     IndividualTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&IndividualTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&IndividualTableType);
     PyModule_AddObject(module, "IndividualTable", (PyObject *) &IndividualTableType);
 
     /* NodeTable type */
     NodeTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&NodeTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&NodeTableType);
     PyModule_AddObject(module, "NodeTable", (PyObject *) &NodeTableType);
 
     /* EdgeTable type */
     EdgeTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&EdgeTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&EdgeTableType);
     PyModule_AddObject(module, "EdgeTable", (PyObject *) &EdgeTableType);
 
     /* MigrationTable type */
     MigrationTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&MigrationTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&MigrationTableType);
     PyModule_AddObject(module, "MigrationTable", (PyObject *) &MigrationTableType);
 
     /* SiteTable type */
     SiteTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&SiteTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&SiteTableType);
     PyModule_AddObject(module, "SiteTable", (PyObject *) &SiteTableType);
 
     /* MutationTable type */
     MutationTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&MutationTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&MutationTableType);
     PyModule_AddObject(module, "MutationTable", (PyObject *) &MutationTableType);
 
     /* PopulationTable type */
     PopulationTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&PopulationTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&PopulationTableType);
     PyModule_AddObject(module, "PopulationTable", (PyObject *) &PopulationTableType);
 
     /* ProvenanceTable type */
     ProvenanceTableType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&ProvenanceTableType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&ProvenanceTableType);
     PyModule_AddObject(module, "ProvenanceTable", (PyObject *) &ProvenanceTableType);
 
     /* TableCollectionTable type */
     TableCollectionType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&TableCollectionType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&TableCollectionType);
     PyModule_AddObject(module, "TableCollection", (PyObject *) &TableCollectionType);
 
     /* TreeSequence type */
     TreeSequenceType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&TreeSequenceType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&TreeSequenceType);
     PyModule_AddObject(module, "TreeSequence", (PyObject *) &TreeSequenceType);
 
     /* Tree type */
     TreeType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&TreeType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&TreeType);
     PyModule_AddObject(module, "Tree", (PyObject *) &TreeType);
 
     /* TreeDiffIterator type */
     TreeDiffIteratorType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&TreeDiffIteratorType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&TreeDiffIteratorType);
     PyModule_AddObject(module, "TreeDiffIterator", (PyObject *) &TreeDiffIteratorType);
 
     /* VcfConverter type */
     VcfConverterType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&VcfConverterType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&VcfConverterType);
     PyModule_AddObject(module, "VcfConverter", (PyObject *) &VcfConverterType);
 
     /* HaplotypeGenerator type */
     HaplotypeGeneratorType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&HaplotypeGeneratorType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&HaplotypeGeneratorType);
     PyModule_AddObject(module, "HaplotypeGenerator",
@@ -8610,15 +8586,15 @@ init_tskit(void)
     /* VariantGenerator type */
     VariantGeneratorType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&VariantGeneratorType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&VariantGeneratorType);
     PyModule_AddObject(module, "VariantGenerator", (PyObject *) &VariantGeneratorType);
 
     /* LdCalculator type */
     LdCalculatorType.tp_new = PyType_GenericNew;
     if (PyType_Ready(&LdCalculatorType) < 0) {
-        INITERROR;
+        return NULL;
     }
     Py_INCREF(&LdCalculatorType);
     PyModule_AddObject(module, "LdCalculator", (PyObject *) &LdCalculatorType);
@@ -8652,7 +8628,5 @@ init_tskit(void)
     PyModule_AddIntConstant(module, "FORWARD", TSK_DIR_FORWARD);
     PyModule_AddIntConstant(module, "REVERSE", TSK_DIR_REVERSE);
 
-#if PY_MAJOR_VERSION >= 3
     return module;
-#endif
 }

python/requirements/conda-minimal.txt

@@ -1,7 +1,6 @@
 numpy
 nose
 h5py
-six
 jsonschema
 svgwrite
 msprime

python/requirements/development.txt

@@ -6,12 +6,12 @@ mock
 newick
 nose
 numpy
-six
 kastore
 jsonschema
 sphinx
 sphinx-argparse
 sphinx_rtd_theme
+sphinx-issues
 breathe
 svgwrite
 pyparsing