Make optional dependencies default on CPython

14 files changed, 56 insertions, 74 deletions

diff --git a/.appveyor.yml b/.appveyor.yml
index d3d5c0e5..1ee02839 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -12,15 +12,15 @@ environment:
 
   matrix:
     - PYTHON: "C:\\Python36-x64"
-      PYTHON_VERSION: "3.6.8"
+      PYTHON_VERSION: "3.6"
       PYTHON_ARCH: "64"
 
     - PYTHON: "C:\\Python37-x64"
-      PYTHON_VERSION: "3.7.5"
+      PYTHON_VERSION: "3.7"
       PYTHON_ARCH: "64"
 
     - PYTHON: "C:\\Python38-x64"
-      PYTHON_VERSION: "3.8.0"
+      PYTHON_VERSION: "3.8"
       PYTHON_ARCH: "64"
       PIP_FLAGS: "--pre"
 
@@ -34,12 +34,8 @@ install:
   - "python --version"
   - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
 
-  # install required packages
-  - "pip install --cache-dir=%CACHE_DIR% %PIP_FLAGS% -r requirements.txt"
-  - "pip install --cache-dir=%CACHE_DIR% %PIP_FLAGS% -r requirements/optional.txt"
-
   # Install the build and runtime dependencies of the project.
-  # - "%CMD_IN_ENV% pip install --timeout=60 -r requirements.txt"
+  - "python -m pip install --upgrade pip wheel setuptools"
   - "pip install ."
 
 # Not a .NET project, we build networkx in the install step instead
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b5097ddb..53781693 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -30,10 +30,9 @@ jobs:
           command: |
             python3 -m venv venv
             source venv/bin/activate
-            pip install --upgrade pip
+            pip install --upgrade pip wheel setuptools
             pip install -r requirements.txt
             pip install -r requirements/doc.txt
-            pip install -r requirements/optional.txt
             pip install pydot pygraphviz
 
       - run:
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 3032d063..8828c483 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -1,3 +1,5 @@
+name: macOS tests
+
 on:
   push:
     branches: [ master ]
@@ -6,7 +8,6 @@ on:
 
 jobs:
   test_macos:
-    name: macOS tests
     runs-on: macos-latest
     strategy:
       max-parallel: 3
@@ -28,7 +29,6 @@ jobs:
       run: |
         pip install --upgrade pip wheel setuptools
         pip install -r requirements.txt
-        pip install -r requirements/optional.txt
         pip install pydot pygraphviz
         pip install .
         pip list
diff --git a/.travis.yml b/.travis.yml
index d0d9c58f..38fe09af 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,7 +8,7 @@ cache: pip
 matrix:
   include:
     - os: linux
-      python: 3.7
+      python: 3.6
       env:
       - OPTIONAL_DEPS=1
       - MINIMUM_REQUIREMENTS=1
@@ -42,15 +42,9 @@ matrix:
           packages:
           - libgdal-dev
           - graphviz
-    - python: 3.6
-    - python: 3.7
     - python: 3.8
     - python: 3.9-dev
-      env:
-      - MIN_DEPS=1
-    - python: pypy3.6-7.1.1
-      env:
-      - MIN_DEPS=1
+    - python: pypy3
 
 before_install:
   # prepare the system to install prerequisites or dependencies
@@ -61,13 +55,10 @@ before_install:
 
 install:
   # install required packages
-  - pip install --upgrade pip
+  - pip install --upgrade pip wheel setuptools
   - pip install --retries 3 ${PIP_FLAGS} -r requirements.txt
   - if [[ "${OPTIONAL_DEPS}" == 1 ]]; then
-      pip install --retries 3 ${PIP_FLAGS} -r requirements/optional.txt;
-      pip install --retries 3 ${PIP_FLAGS} -r requirements/extras.txt;
-    elif [[ "${MIN_DEPS}" != 1 ]]; then
-      pip install --retries 3 ${PIP_FLAGS} -r requirements/optional.txt;
+      pip install --retries 3 ${PIP_FLAGS} -r requirements/extra.txt;
     fi
   # install networkx
   - printenv PWD
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 7b40d63c..96b7ae93 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -43,7 +43,7 @@ Development Workflow
          # (Optional) Install pygraphviz, pydot, and gdal packages
          # These packages require that you have your system properly configured
          # and what that involves differs on various systems.
-         # pip install -r requirements/extras.txt
+         # pip install -r requirements/extra.txt
          #
          # Build and install networkx from source
          pip install -e .
@@ -64,7 +64,7 @@ Development Workflow
          # (Optional) Install pygraphviz, pydot, and gdal packages
          # These packages require that you have your system properly configured
          # and what that involves differs on various systems.
-         # pip install -r requirements/extras.txt
+         # pip install -r requirements/extra.txt
          #
          # Install networkx from source
          pip install -e . --no-deps
@@ -228,12 +228,22 @@ Guidelines
 * All changes are reviewed.  Ask on the
   `mailing list <http://groups.google.com/group/networkx-discuss>`_ if
   you get no response to your pull request.
+* Default dependencies are listed in ``requirements/default.txt`` and extra
+  (i.e., optional) dependencies are listed in ``requirements/extra.txt``.
+  We don't often add new default and extra dependencies.  If you are considering
+  adding code that has a dependency, you should first consider adding a gallery
+  example.  Typically, new proposed dependencies would first be added as extra
+  dependencies.  Extra dependencies should be easy to install on all platforms
+  and widely-used.  New default dependencies should be easy to install on all
+  platforms, widely-used in the community, and have demonstrated potential for
+  wide-spread use in NetworkX.
 * Use the following import conventions::
 
    import numpy as np
    import scipy as sp
    import matplotlib as mpl
    import matplotlib.pyplot as plt
+   import pandas as pd 
    import networkx as nx
 
 * Use the decorator ``not_implemented_for`` in ``networkx/utils/decorators.py``
diff --git a/INSTALL.rst b/INSTALL.rst
index ed9e8c50..d5128675 100644
--- a/INSTALL.rst
+++ b/INSTALL.rst
@@ -65,28 +65,18 @@ Then, if you want to update ``networkx`` at any time, in the same directory do::
 
     $ git pull
 
-Optional packages
------------------
+Extra packages
+--------------
 
 .. note::
    Some optional packages (e.g., `gdal`) may require compiling
    C or C++ code.  If you have difficulty installing these packages
-   with `pip`, please review the instructions for installing
-   the full `scientific Python stack <https://scipy.org/install.html>`_.
+   with `pip`, please consult the homepages of those packages.
 
-The following optional packages provide additional functionality. See the
+The following extra packages provide additional functionality. See the
 files in the ``requirements/`` directory for information about specific
 version requirements.
 
-- `NumPy <http://www.numpy.org/>`_ provides array-based dense 
-  matrix representations of graphs and high-performance array math and linear
-  algebra which is used in some graph algorithms.
-- `SciPy <http://scipy.org/>`_ provides sparse matrix representation
-  of graphs and many numerical scientific tools.
-- `pandas <http://pandas.pydata.org/>`_ provides a DataFrame, which
-  is a tabular data structure with labeled axes.
-- `Matplotlib <http://matplotlib.org/>`_ provides flexible drawing of
-  graphs.
 - `PyGraphviz <http://pygraphviz.github.io/>`_ and
   `pydot <https://github.com/erocarrera/pydot>`_ provide graph drawing
   and graph layout algorithms via `GraphViz <http://graphviz.org/>`_.
@@ -94,17 +84,17 @@ version requirements.
 - `gdal <http://www.gdal.org/>`_ provides shapefile format reading and writing.
 - `lxml <http://lxml.de/>`_ used for GraphML XML format.
 
-To install ``networkx`` and all optional packages, do::
+To install ``networkx`` and extra packages, do::
 
-    $ pip install networkx[all]
+    $ pip install networkx[extra]
 
 To explicitly install all optional packages, do::
 
-    $ pip install numpy scipy pandas matplotlib pygraphviz pydot pyyaml gdal
+    $ pip install pygraphviz pydot pyyaml gdal lxml
 
-Or, install any optional package (e.g., ``numpy``) individually::
+Or, install any optional package (e.g., ``pygraphviz``) individually::
 
-    $ pip install numpy
+    $ pip install pygraphviz
 
 Testing
 -------
diff --git a/README.rst b/README.rst
index 94c765dc..badf4bbf 100644
--- a/README.rst
+++ b/README.rst
@@ -10,6 +10,9 @@ NetworkX
 .. image:: https://travis-ci.org/networkx/networkx.svg?branch=master
    :target: https://travis-ci.org/networkx/networkx
 
+.. image:: https://github.com/networkx/networkx/workflows/macOS%20tests/badge.svg?branch=master
+  :target: https://github.com/networkx/networkx/actions?query=workflow%3A%22macOS+tests%22
+
 .. image:: https://ci.appveyor.com/api/projects/status/github/networkx/networkx?branch=master&svg=true
    :target: https://ci.appveyor.com/project/dschult/networkx-pqott
 
diff --git a/doc/release/release_dev.rst b/doc/release/release_dev.rst
index 2dae5e5f..08a7f130 100644
--- a/doc/release/release_dev.rst
+++ b/doc/release/release_dev.rst
@@ -17,6 +17,7 @@ Highlights
 This release is the result of X of work with over X pull requests by
 X contributors. Highlights include:
 
+- NumPy, SciPy, Matplotlib, and pandas are now default requirements.
 
 Improvements
 ------------
diff --git a/requirements/README.md b/requirements/README.md
index ee23aa30..7ee5c66f 100644
--- a/requirements/README.md
+++ b/requirements/README.md
@@ -4,9 +4,7 @@
 
 - [`default.txt`](default.txt)
   Default requirements
-- [`optional.txt`](optional.txt)
-  Optional requirements that are easy to install
-- [`extras.txt`](extras.txt)
+- [`extra.txt`](extra.txt)
   Optional requirements that may require extra steps to install
 - [`test.txt`](test.txt)
   Requirements for running test suite
diff --git a/requirements/default.txt b/requirements/default.txt
index 570c163c..f3d97c9d 100644
--- a/requirements/default.txt
+++ b/requirements/default.txt
@@ -1 +1,5 @@
 decorator>=4.3.0
+numpy>=1.19
+scipy>=1.4
+matplotlib>=3.2
+pandas>=1.0
diff --git a/requirements/extras.txt b/requirements/extra.txt
index 3b7ccd86..640e0961 100644
--- a/requirements/extras.txt
+++ b/requirements/extra.txt
@@ -1,2 +1,4 @@
+lxml>=4.5
 pygraphviz>=1.5, <2.0
 pydot>=1.4.1
+pyyaml>=5.3
diff --git a/requirements/optional.txt b/requirements/optional.txt
deleted file mode 100644
index 196309ce..00000000
--- a/requirements/optional.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-numpy>=1.19
-scipy>=1.4
-pandas>=1.0
-matplotlib>=3.2
-pyyaml>=5.3
-lxml>=4.5
diff --git a/setup.py b/setup.py
index 398b3d99..6e9106bd 100644
--- a/setup.py
+++ b/setup.py
@@ -124,29 +124,23 @@ package_data = {
     "networkx.utils": ["tests/*.py"],
 }
 
-install_requires = ["decorator>=4.3.0"]
+install_requires = [
+    "decorator>=4.3.0",
+    "numpy>=1.19; platform_python_implementation!='PyPy' and python_version<'3.9'",
+    "scipy>=1.4; platform_python_implementation!='PyPy' and python_version<'3.9'",
+    "matplotlib>=3.2; platform_python_implementation!='PyPy' and python_version<'3.9'",
+    "pandas>=1.0; platform_python_implementation!='PyPy' and python_version<'3.9'",
+]
 extras_require = {
-    "all": [
-        "numpy",
-        "scipy",
-        "pandas",
-        "matplotlib",
-        "pygraphviz",
-        "pydot",
-        "pyyaml",
-        "lxml",
-        "pytest",
+    "extra": [
+        "lxml>=4.5",
+        "pygraphviz>=1.5, <2.0",
+        "pydot>=1.4.1",
+        "pyyaml>=5.3",
     ],
     "gdal": ["gdal"],
-    "lxml": ["lxml"],
-    "matplotlib": ["matplotlib"],
-    "pytest": ["pytest"],
-    "numpy": ["numpy"],
-    "pandas": ["pandas"],
     "pydot": ["pydot"],
     "pygraphviz": ["pygraphviz"],
-    "pyyaml": ["pyyaml"],
-    "scipy": ["scipy"],
 }
 
 with open("README.rst", "r") as fh:
diff --git a/tools/travis/before_install.sh b/tools/travis/before_install.sh
index a03aba8e..910bf920 100755
--- a/tools/travis/before_install.sh
+++ b/tools/travis/before_install.sh
@@ -14,7 +14,7 @@ export -f section_end
 
 if [[ "${MINIMUM_REQUIREMENTS}" == 1 ]]; then
     sed -i 's/>=/==/g' requirements/default.txt
-    sed -i 's/>=/==/g' requirements/extras.txt
+    sed -i 's/>=/==/g' requirements/extra.txt
     sed -i 's/>=/==/g' requirements/test.txt
     sed -i 's/>=/==/g' requirements/doc.txt
 fi