DEPS: Bump numpy to 1.13.3 (#25554)

Author: h-vetinari

.travis.yml

@@ -41,7 +41,7 @@ matrix:
 
     - dist: trusty
       env:
-        - JOB="3.6, coverage" ENV_FILE="ci/deps/travis-36.yaml" PATTERN="((not slow and not network) or (single and db))" PANDAS_TESTING_MODE="deprecate" COVERAGE=true
+        - JOB="3.6, coverage" ENV_FILE="ci/deps/travis-36-cov.yaml" PATTERN="((not slow and not network) or (single and db))" PANDAS_TESTING_MODE="deprecate" COVERAGE=true
 
     # In allow_failures
     - dist: trusty

README.md

@@ -164,7 +164,7 @@ pip install pandas
 ```
 
 ## Dependencies
-- [NumPy](https://www.numpy.org): 1.12.0 or higher
+- [NumPy](https://www.numpy.org): 1.13.3 or higher
 - [python-dateutil](https://labix.org/python-dateutil): 2.5.0 or higher
 - [pytz](https://pythonhosted.org/pytz): 2015.4 or higher
 

ci/azure/windows.yml

@@ -8,7 +8,7 @@ jobs:
     vmImage: ${{ parameters.vmImage }}
   strategy:
     matrix:
-      py36_np14:
+      py36_np15:
         ENV_FILE: ci/deps/azure-windows-36.yaml
         CONDA_PY: "36"
 

ci/deps/azure-35-compat.yaml

@@ -3,23 +3,23 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - beautifulsoup4==4.4.1
-  - bottleneck=1.2.0
-  - cython=0.28.2
-  - hypothesis>=3.58.0
+  - beautifulsoup4=4.4.1
+  - bottleneck=1.2.1
   - jinja2=2.8
-  - numexpr=2.6.1
-  - numpy=1.12.0
+  - numexpr=2.6.2
+  - numpy=1.13.3
   - openpyxl=2.4.0
   - pytables=3.4.2
   - python-dateutil=2.5.0
-  - python=3.5*
+  - python=3.5.*
   - pytz=2015.4
-  - scipy=0.18.1
+  - scipy=0.19.0
   - xlrd=1.0.0
   - xlsxwriter=0.7.7
   - xlwt=1.0.0
   # universal
+  - cython=0.28.2
+  - hypothesis>=3.58.0
   - pytest-xdist
   - pytest-mock
   - isort

ci/deps/azure-36-locale.yaml

@@ -4,15 +4,15 @@ channels:
   - conda-forge
 dependencies:
   - beautifulsoup4==4.5.1
-  - bottleneck=1.2.0
+  - bottleneck=1.2.*
   - cython=0.28.2
   - lxml
-  - matplotlib=2.0.0
-  - numpy=1.12.0
+  - matplotlib=2.2.2
+  - numpy=1.14.*
   - openpyxl=2.4.0
   - python-dateutil
   - python-blosc
-  - python=3.6
+  - python=3.6.*
   - pytz=2016.10
   - scipy
   - sqlalchemy=1.1.4

ci/deps/azure-36-locale_slow.yaml

@@ -10,14 +10,14 @@ dependencies:
   - ipython
   - jinja2
   - lxml
-  - matplotlib
+  - matplotlib=3.0.*
   - nomkl
   - numexpr
-  - numpy
+  - numpy=1.15.*
   - openpyxl
   - pytables
   - python-dateutil
-  - python=3.6*
+  - python=3.6.*
   - pytz
   - s3fs
   - scipy

ci/deps/azure-37-locale.yaml

@@ -16,7 +16,7 @@ dependencies:
   - openpyxl
   - pytables
   - python-dateutil
-  - python=3.7*
+  - python=3.7.*
   - pytz
   - s3fs
   - scipy

ci/deps/azure-37-numpydev.yaml

@@ -2,7 +2,7 @@ name: pandas-dev
 channels:
   - defaults
 dependencies:
-  - python=3.7*
+  - python=3.7.*
   - pytz
   - Cython>=0.28.2
   # universal

ci/deps/azure-macos-35.yaml

@@ -8,14 +8,14 @@ dependencies:
   - html5lib
   - jinja2
   - lxml
-  - matplotlib=2.2.0
+  - matplotlib=2.2.3
   - nomkl
   - numexpr
-  - numpy=1.12.0
+  - numpy=1.13.3
   - openpyxl
   - pyarrow
   - pytables
-  - python=3.5*
+  - python=3.5.*
   - pytz
   - xarray
   - xlrd

ci/deps/azure-windows-36.yaml

@@ -7,9 +7,9 @@ dependencies:
   - bottleneck
   - boost-cpp<1.67
   - fastparquet>=0.2.1
-  - matplotlib
+  - matplotlib=3.0.2
   - numexpr
-  - numpy=1.14*
+  - numpy=1.15.*
   - openpyxl
   - parquet-cpp
   - pyarrow

ci/deps/azure-windows-37.yaml

@@ -9,7 +9,7 @@ dependencies:
   - html5lib
   - jinja2
   - lxml
-  - matplotlib=3.0.1
+  - matplotlib=2.2.*
   - numexpr
   - numpy=1.14.*
   - openpyxl

ci/deps/travis-36.yaml renamed to ci/deps/travis-36-cov.yaml

@@ -14,14 +14,15 @@ dependencies:
   - matplotlib
   - nomkl
   - numexpr
-  - numpy
+  - numpy=1.15.*
   - openpyxl
+  - pandas-gbq
   - psycopg2
   - pyarrow=0.9.0
   - pymysql
   - pytables
   - python-snappy
-  - python=3.6.6
+  - python=3.6.*
   - pytz
   - s3fs
   - scikit-learn

ci/deps/travis-36-doc.yaml

@@ -29,7 +29,7 @@ dependencies:
   - pytables
   - python-dateutil
   - python-snappy
-  - python=3.6*
+  - python=3.6.*
   - pytz
   - scipy
   - seaborn

ci/deps/travis-36-locale.yaml

@@ -4,26 +4,33 @@ channels:
   - conda-forge
 dependencies:
   - beautifulsoup4
+  - blosc=1.14.3
+  - python-blosc
   - cython>=0.28.2
+  - fastparquet=0.2.1
+  - gcsfs=0.1.0
   - html5lib
   - ipython
   - jinja2
-  - lxml
-  - matplotlib
+  - lxml=3.7.0
+  - matplotlib=3.0.0
   - nomkl
   - numexpr
   - numpy
   - openpyxl
-  - psycopg2
+  - pandas-gbq=0.8.0
+  - psycopg2=2.6.2
   - pymysql=0.7.9
   - pytables
   - python-dateutil
-  - python=3.6*
+  # cannot go past python=3.6.6 for matplotlib=3.0.0 due to
+  # https://github.com/matplotlib/matplotlib/issues/12626
+  - python=3.6.6
   - pytz
-  - s3fs
+  - s3fs=0.0.8
   - scipy
-  - sqlalchemy
-  - xarray
+  - sqlalchemy=1.1.4
+  - xarray=0.8.2
   - xlrd
   - xlsxwriter
   - xlwt

ci/deps/travis-36-slow.yaml

@@ -16,7 +16,7 @@ dependencies:
   - pymysql
   - pytables
   - python-dateutil
-  - python=3.6*
+  - python=3.6.*
   - pytz
   - s3fs
   - scipy

ci/deps/travis-37.yaml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - c3i_test
 dependencies:
-  - python=3.7
+  - python=3.7.*
   - botocore>=1.11
   - cython>=0.28.2
   - numpy

doc/source/install.rst

@@ -224,7 +224,7 @@ Dependencies
 ------------
 
 * `setuptools <https://setuptools.readthedocs.io/en/latest/>`__: 24.2.0 or higher
-* `NumPy <http://www.numpy.org>`__: 1.12.0 or higher
+* `NumPy <http://www.numpy.org>`__: 1.13.3 or higher
 * `python-dateutil <https://dateutil.readthedocs.io/en/stable/>`__: 2.5.0 or higher
 * `pytz <http://pytz.sourceforge.net/>`__: 2015.4 or higher
 
@@ -235,11 +235,11 @@ Recommended Dependencies
 
 * `numexpr <https://github.com/pydata/numexpr>`__: for accelerating certain numerical operations.
   ``numexpr`` uses multiple cores as well as smart chunking and caching to achieve large speedups.
-  If installed, must be Version 2.6.1 or higher.
+  If installed, must be Version 2.6.2 or higher.
 
 * `bottleneck <https://github.com/kwgoodman/bottleneck>`__: for accelerating certain types of ``nan``
   evaluations. ``bottleneck`` uses specialized cython routines to achieve large speedups. If installed,
-  must be Version 1.2.0 or higher.
+  must be Version 1.2.1 or higher.
 
 .. note::
 
@@ -254,27 +254,27 @@ Optional Dependencies
 
 * `Cython <http://www.cython.org>`__: Only necessary to build development
   version. Version 0.28.2 or higher.
-* `SciPy <http://www.scipy.org>`__: miscellaneous statistical functions, Version 0.18.1 or higher
-* `xarray <http://xarray.pydata.org>`__: pandas like handling for > 2 dims. Version 0.7.0 or higher is recommended.
+* `SciPy <http://www.scipy.org>`__: miscellaneous statistical functions, Version 0.19.0 or higher
+* `xarray <http://xarray.pydata.org>`__: pandas like handling for > 2 dims. Version 0.8.2 or higher is recommended.
 * `PyTables <http://www.pytables.org>`__: necessary for HDF5-based storage, Version 3.4.2 or higher
 * `pyarrow <http://arrow.apache.org/docs/python/>`__ (>= 0.9.0): necessary for feather-based storage.
-* `Apache Parquet <https://parquet.apache.org/>`__, either `pyarrow <http://arrow.apache.org/docs/python/>`__ (>= 0.7.0) or `fastparquet <https://fastparquet.readthedocs.io/en/latest>`__ (>= 0.2.1) for parquet-based storage. The `snappy <https://pypi.org/project/python-snappy>`__ and `brotli <https://pypi.org/project/brotlipy>`__ are available for compression support.
+* `Apache Parquet <https://parquet.apache.org/>`__, either `pyarrow <http://arrow.apache.org/docs/python/>`__ (>= 0.9.0) or `fastparquet <https://fastparquet.readthedocs.io/en/latest>`__ (>= 0.2.1) for parquet-based storage. The `snappy <https://pypi.org/project/python-snappy>`__ and `brotli <https://pypi.org/project/brotlipy>`__ are available for compression support.
 * `SQLAlchemy <http://www.sqlalchemy.org>`__: for SQL database support. Version 1.1.4 or higher recommended. Besides SQLAlchemy, you also need a database specific driver. You can find an overview of supported drivers for each SQL dialect in the `SQLAlchemy docs <http://docs.sqlalchemy.org/en/latest/dialects/index.html>`__. Some common drivers are:
 
     * `psycopg2 <http://initd.org/psycopg/>`__: for PostgreSQL
     * `pymysql <https://github.com/PyMySQL/PyMySQL>`__: for MySQL.
     * `SQLite <https://docs.python.org/3/library/sqlite3.html>`__: for SQLite, this is included in Python's standard library by default.
 
-* `matplotlib <http://matplotlib.org/>`__: for plotting, Version 2.0.0 or higher.
+* `matplotlib <http://matplotlib.org/>`__: for plotting, Version 2.2.2 or higher.
 * For Excel I/O:
 
     * `xlrd/xlwt <http://www.python-excel.org/>`__: Excel reading (xlrd), version 1.0.0 or higher required, and writing (xlwt)
     * `openpyxl <https://openpyxl.readthedocs.io/en/stable/>`__: openpyxl version 2.4.0
-      for writing .xlsx files (xlrd >= 0.9.0)
+      for writing .xlsx files (xlrd >= 1.0.0)
     * `XlsxWriter <https://pypi.org/project/XlsxWriter>`__: Alternative Excel writer
 
 * `Jinja2 <http://jinja.pocoo.org/>`__: Template engine for conditional HTML formatting.
-* `s3fs <http://s3fs.readthedocs.io/>`__: necessary for Amazon S3 access (s3fs >= 0.0.7).
+* `s3fs <http://s3fs.readthedocs.io/>`__: necessary for Amazon S3 access (s3fs >= 0.0.8).
 * `blosc <https://pypi.org/project/blosc>`__: for msgpack compression using ``blosc``
 * `gcsfs <http://gcsfs.readthedocs.io/>`__: necessary for Google Cloud Storage access (gcsfs >= 0.1.0).
 * One of
@@ -289,8 +289,6 @@ Optional Dependencies
   <https://pandas-gbq.readthedocs.io/en/latest/install.html#dependencies>`__:
   for Google BigQuery I/O. (pandas-gbq >= 0.8.0)
 
-
-* `Backports.lzma <https://pypi.org/project/backports.lzma/>`__: Only for Python 2, for writing to and/or reading from an xz compressed DataFrame in CSV; Python 3 support is built into the standard library.
 * One of the following combinations of libraries is needed to use the
   top-level :func:`~pandas.read_html` function:
 

doc/source/whatsnew/v0.25.0.rst

@@ -159,30 +159,54 @@ cause a ``SparseSeries`` or ``SparseDataFrame`` to be returned, as before.
 Increased minimum versions for dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Due to dropping support for Python 2.7, a number of optional dependencies have updated minimum versions.
-Independently, some minimum supported versions of dependencies were updated (:issue:`23519`, :issue:`24942`).
+Due to dropping support for Python 2.7, a number of optional dependencies have updated minimum versions (issue:`25725`, :issue:`24942`, :issue:`25752`).
+Independently, some minimum supported versions of dependencies were updated (:issue:`23519`, :issue:`25554`).
 If installed, we now require:
 
 +-----------------+-----------------+----------+
 | Package         | Minimum Version | Required |
 +=================+=================+==========+
-| beautifulsoup4  | 4.4.1           |          |
+| numpy           | 1.13.3          |    X     |
 +-----------------+-----------------+----------+
-| openpyxl        | 2.4.0           |          |
+| pytz            | 2015.4          |    X     |
 +-----------------+-----------------+----------+
-| pymysql         | 0.7.9           |          |
+| bottleneck      | 1.2.1           |          |
 +-----------------+-----------------+----------+
-| pytz            | 2015.4          |          |
-+-----------------+-----------------+----------+
-| sqlalchemy      | 1.1.4           |          |
-+-----------------+-----------------+----------+
-| xlsxwriter      | 0.7.7           |          |
-+-----------------+-----------------+----------+
-| xlwt            | 1.0.0           |          |
+| numexpr         | 2.6.2           |          |
 +-----------------+-----------------+----------+
 | pytest (dev)    | 4.0.2           |          |
 +-----------------+-----------------+----------+
 
+For `optional libraries <https://pandas-docs.github.io/pandas-docs-travis/install.html#dependencies>`_ the general recommendation is to use the latest version.
+The following table lists the lowest version per library that is currently being tested throughout the development of pandas.
+Optional libraries below the lowest tested version may still work, but are not considered supported.
+
++-----------------+-----------------+
+| Package         | Minimum Version |
++=================+=================+
+| fastparquet     | 0.2.1           |
++-----------------+-----------------+
+| matplotlib      | 2.2.2           |
++-----------------+-----------------+
+| openpyxl        | 2.4.0           |
++-----------------+-----------------+
+| pyarrow         | 0.9.0           |
++-----------------+-----------------+
+| pytables        | 3.4.2           |
++-----------------+-----------------+
+| scipy           | 0.19.0          |
++-----------------+-----------------+
+| sqlalchemy      | 1.1.4           |
++-----------------+-----------------+
+| xarray          | 0.8.2           |
++-----------------+-----------------+
+| xlrd            | 1.0.0           |
++-----------------+-----------------+
+| xlsxwriter      | 0.7.7           |
++-----------------+-----------------+
+| xlwt            | 1.0.0           |
++-----------------+-----------------+
+
 .. _whatsnew_0250.api.other:
 
 Other API Changes

environment.yml

@@ -31,14 +31,14 @@ dependencies:
   - blosc
   - botocore>=1.11
   - boto3
-  - bottleneck>=1.2.0
+  - bottleneck>=1.2.1
   - fastparquet>=0.2.1
   - html5lib
   - ipython>=5.6.0
   - ipykernel
   - jinja2
   - lxml
-  - matplotlib>=2.0.0
+  - matplotlib>=2.2.2
   - nbsphinx
   - numexpr>=2.6.8
   - openpyxl