Merge pull request #329 from iiasa/issue/319

Clean up prior to 3.0.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,7 @@ to ensure that the PR does what it intends.
 <!-- For example:
 
 - Run a specific code snippet or command and check the output.
-- Build the documentation and look at a certain.
+- Build the documentation and look at a certain page.
 - Simply view changes and note that the CI checks all pass.
 - Ensure that changes/additions are self-documenting, i.e. that another
   developer like the reviewer will be able to understand what the code does
@@ -36,9 +36,8 @@ In ambiguous cases, strike them out and add a short explanation, e.g.
 - [ ] Tests added.
 - [ ] Documentation added.
 - [ ] Release notes updated.
-  <!-- To update `RELEASE_NOTES.rst`, add a single line under the section
-  “Next release” similar to:
+  <!-- Add a single line at the top of the “Next release” section of
+       RELEASE_NOTES.rst, where '999' is the GitHub pull request number:
 
-  - `#999 <https://github.com/iiasa/ixmp/pull/999>`_: Title or single-sentence
-    description from above.
+    - :pull:`999`: Title or single-sentence description from above.
   -->

.readthedocs.yml

@@ -0,0 +1,7 @@
+version: 2
+
+python:
+  install:
+  - method: pip
+    path: .
+    extra_requirements: [docs, tests, tutorial]

.travis.yml

@@ -61,9 +61,7 @@ script:
   # Run tests. These include the equivalent of Travis R tests via test_r.py.
   - pytest ixmp -m 'rixmp or not performance' --verbose --cov-report=xml
   # Test that documentation can be built
-  - cd doc
-  - pip install -r requirements.txt
-  - make html
+  - make --directory=doc html
 
 after_success:
   - codecov

MANIFEST.in

@@ -1,3 +1,3 @@
-include versioneer.py
-include ixmp/_version.py
-include ixmp/model/dantzig.gms
+exclude .*
+prune .github
+prune ci

README.md

@@ -3,7 +3,7 @@
 [![PyPI version](https://img.shields.io/pypi/v/ixmp.svg)](https://pypi.python.org/pypi/ixmp/)
 [![Anaconda version](https://img.shields.io/conda/vn/conda-forge/ixmp)](https://anaconda.org/conda-forge/ixmp)
 [![Documentation build](https://readthedocs.com/projects/iiasa-energy-program-ixmp/badge/?version=master)](https://message.iiasa.ac.at/projects/ixmp/en/master/)
-[![Build status](https://travis-ci.org/iiasa/ixmp.svg?branch=master)](https://travis-ci.org/iiasa/ixmp)
+[![Build status](https://travis-ci.com/iiasa/ixmp.svg?branch=master)](https://travis-ci.com/iiasa/ixmp)
 [![Test coverage](https://codecov.io/gh/iiasa/ixmp/branch/master/graph/badge.svg)](https://codecov.io/gh/iiasa/ixmp)
 
 ## Overview

RELEASE_NOTES.rst

@@ -10,32 +10,32 @@ Migration notes
 All changes
 -----------
 
-- `#327 <https://github.com/iiasa/ixmp/pull/327>`_: Bump JPype dependency to 0.7.5.
-- `#298 <https://github.com/iiasa/ixmp/pull/298>`_: Improve memory management in :class:`.JDBCBackend`.
-- `#316 <https://github.com/iiasa/ixmp/pull/316>`_: Raise user-friendly exceptions from :meth:`.Reporter.get` in Jupyter notebooks and other read–evaluate–print loops (REPLs).
-- `#315 <https://github.com/iiasa/ixmp/pull/315>`_: Ensure :meth:`.Model.initialize` is always called for new *and* cloned objects.
-- `#320 <https://github.com/iiasa/ixmp/pull/320>`_: Add CLI command `ixmp show-versions` to print ixmp and dependency versions for debugging.
-- `#314 <https://github.com/iiasa/ixmp/pull/314>`_: Bulk saving for metadata and exposing documentation API
-- `#312 <https://github.com/iiasa/ixmp/pull/312>`_: Add :meth:`~.computations.apply_units`, :meth:`~computations.select` reporting calculations; expand :meth:`.Reporter.add`.
-- `#310 <https://github.com/iiasa/ixmp/pull/310>`_: :meth:`.Reporter.add_product` accepts a :class:`.Key` with a tag; :func:`~.computations.aggregate` preserves :class:`.Quantity` attributes.
-- `#304 <https://github.com/iiasa/ixmp/pull/304>`_: Add CLI command ``ixmp solve`` to run model solver.
-- `#303 <https://github.com/iiasa/ixmp/pull/303>`_: Add `dims` and `units` arguments to :meth:`Reporter.add_file`; remove :meth:`Reporter.read_config` (redundant with :meth:`Reporter.configure`).
-- `#295 <https://github.com/iiasa/ixmp/pull/295>`_: Add option to include `subannual` column in dataframe returned by :meth:`.TimeSeries.timeseries`.
-- `#286 <https://github.com/iiasa/ixmp/pull/286>`_,
-  `#297 <https://github.com/iiasa/ixmp/pull/297>`_,
-  `#309 <https://github.com/iiasa/ixmp/pull/309>`_: Add :meth:`.Scenario.to_excel` and :meth:`.read_excel`; this functionality is transferred to ixmp from :mod:`message_ix` and enhanced for dealing with maximum row limits in Excel.
-- `#270 <https://github.com/iiasa/ixmp/pull/270>`_: Include all tests in the ixmp package.
-- `#212 <https://github.com/iiasa/ixmp/pull/212>`_: Add :meth:`Model.initialize` API to help populate new Scenarios according to a model scheme.
-- `#267 <https://github.com/iiasa/ixmp/pull/267>`_: Apply units to reported quantities.
-- `#254 <https://github.com/iiasa/ixmp/pull/254>`_: Remove deprecated items:
+- :pull:`327`: Bump JPype dependency to 0.7.5.
+- :pull:`298`: Improve memory management in :class:`.JDBCBackend`.
+- :pull:`316`: Raise user-friendly exceptions from :meth:`.Reporter.get` in Jupyter notebooks and other read–evaluate–print loops (REPLs).
+- :pull:`315`: Ensure :meth:`.Model.initialize` is always called for new *and* cloned objects.
+- :pull:`320`: Add CLI command `ixmp show-versions` to print ixmp and dependency versions for debugging.
+- :pull:`314`: Bulk saving for metadata and exposing documentation API
+- :pull:`312`: Add :meth:`~.computations.apply_units`, :meth:`~computations.select` reporting calculations; expand :meth:`.Reporter.add`.
+- :pull:`310`: :meth:`.Reporter.add_product` accepts a :class:`.Key` with a tag; :func:`~.computations.aggregate` preserves :class:`.Quantity` attributes.
+- :pull:`304`: Add CLI command ``ixmp solve`` to run model solver.
+- :pull:`303`: Add `dims` and `units` arguments to :meth:`Reporter.add_file`; remove :meth:`Reporter.read_config` (redundant with :meth:`Reporter.configure`).
+- :pull:`295`: Add option to include `subannual` column in dataframe returned by :meth:`.TimeSeries.timeseries`.
+- :pull:`286`,
+  :pull:`297`,
+  :pull:`309`: Add :meth:`.Scenario.to_excel` and :meth:`.read_excel`; this functionality is transferred to ixmp from :mod:`message_ix` and enhanced for dealing with maximum row limits in Excel.
+- :pull:`270`: Include all tests in the ixmp package.
+- :pull:`212`: Add :meth:`Model.initialize` API to help populate new Scenarios according to a model scheme.
+- :pull:`267`: Apply units to reported quantities.
+- :pull:`254`: Remove deprecated items:
 
   - ~/.local/ixmp as a configuration location.
   - positional and ``dbtype=`` arguments to :class:`.Platform`/:class:`.JDBCBackend`.
   - ``first_model_year=``, ``keep_sol=``, and ``scen=`` arguments to :meth:`~.Scenario.clone`.
   - ``rixmp.legacy``, an earlier version of :ref:`the R interface <rixmp>` that did not use reticulate.
-- `#261 <https://github.com/iiasa/ixmp/pull/261>`_: Increase minimum pandas version to 1.0; adjust for `API changes and deprecations <https://pandas.pydata.org/pandas-docs/version/1.0.0/whatsnew/v1.0.0.html#backwards-incompatible-api-changes>`_.
-- `#243 <https://github.com/iiasa/ixmp/pull/243>`_: Add :meth:`.export_timeseries_data` to write data for multiple scenarios to CSV.
-- `#264 <https://github.com/iiasa/ixmp/pull/264>`_: Implement methods to get and create new subannual timeslices.
+- :pull:`261`: Increase minimum pandas version to 1.0; adjust for `API changes and deprecations <https://pandas.pydata.org/pandas-docs/version/1.0.0/whatsnew/v1.0.0.html#backwards-incompatible-api-changes>`_.
+- :pull:`243`: Add :meth:`.export_timeseries_data` to write data for multiple scenarios to CSV.
+- :pull:`264`: Implement methods to get and create new subannual timeslices.
 
 v2.0.0 (2020-01-14)
 ===================
@@ -75,25 +75,25 @@ DEFAULT_LOCAL_DB_PATH
 All changes
 -----------
 
-- `#240 <https://github.com/iiasa/ixmp/pull/240>`_: Add ``ixmp list`` command-line tool.
-- `#225 <https://github.com/iiasa/ixmp/pull/225>`_: Ensure filters are always converted to string.
-- `#189 <https://github.com/iiasa/ixmp/pull/189>`_: Identify and load Scenarios using URLs.
-- `#182 <https://github.com/iiasa/ixmp/pull/182>`_,
-  `#200 <https://github.com/iiasa/ixmp/pull/200>`_,
-  `#213 <https://github.com/iiasa/ixmp/pull/213>`_,
-  `#217 <https://github.com/iiasa/ixmp/pull/217>`_,
-  `#230 <https://github.com/iiasa/ixmp/pull/230>`_,
-  `#245 <https://github.com/iiasa/ixmp/pull/245>`_,
-  `#246 <https://github.com/iiasa/ixmp/pull/246>`_: Add new Backend, Model APIs and CachingBackend, JDBCBackend, GAMSModel classes.
-- `#188 <https://github.com/iiasa/ixmp/pull/188>`_,
-  `#195 <https://github.com/iiasa/ixmp/pull/195>`_: Enhance reporting.
-- `#177 <https://github.com/iiasa/ixmp/pull/177>`_: Add ability to pass `gams_args` through :meth:`.solve`.
-- `#175 <https://github.com/iiasa/ixmp/pull/175>`_,
-  `#239 <https://github.com/iiasa/ixmp/pull/239>`_: Drop support for Python 2.7.
-- `#174 <https://github.com/iiasa/ixmp/pull/174>`_: Set `convertStrings=True` for JPype >= 0.7; see the `JPype changelog <https://jpype.readthedocs.io/en/latest/CHANGELOG.html>`_.
-- `#173 <https://github.com/iiasa/ixmp/pull/173>`_: Make AppVeyor CI more robust; support pandas 0.25.0.
-- `#165 <https://github.com/iiasa/ixmp/pull/165>`_: Add support for handling geodata.
-- `#232 <https://github.com/iiasa/ixmp/pull/232>`_: Fix exposing whole config file to log output.
+- :pull:`240`: Add ``ixmp list`` command-line tool.
+- :pull:`225`: Ensure filters are always converted to string.
+- :pull:`189`: Identify and load Scenarios using URLs.
+- :pull:`182`,
+  :pull:`200`,
+  :pull:`213`,
+  :pull:`217`,
+  :pull:`230`,
+  :pull:`245`,
+  :pull:`246`: Add new Backend, Model APIs and CachingBackend, JDBCBackend, GAMSModel classes.
+- :pull:`188`,
+  :pull:`195`: Enhance reporting.
+- :pull:`177`: Add ability to pass `gams_args` through :meth:`.solve`.
+- :pull:`175`,
+  :pull:`239`: Drop support for Python 2.7.
+- :pull:`174`: Set `convertStrings=True` for JPype >= 0.7; see the `JPype changelog <https://jpype.readthedocs.io/en/latest/CHANGELOG.html>`_.
+- :pull:`173`: Make AppVeyor CI more robust; support pandas 0.25.0.
+- :pull:`165`: Add support for handling geodata.
+- :pull:`232`: Fix exposing whole config file to log output.
 
 v0.2.0 (2019-06-25)
 ===================
@@ -109,34 +109,34 @@ Release 0.2.0 coincides with MESSAGEix release 1.2.0.
 All changes
 -----------
 
-- `#135 <https://github.com/iiasa/ixmp/pull/135>`_: Test ``rixmp`` (former ``retixmp``) using the R ``testthat`` package.
-- `#142 <https://github.com/iiasa/ixmp/pull/142>`_: Cloning across platforms, better support of IAMC_style timeseries data, preparations for MESSAGEix release 1.2 in Java core.
-- `#115 <https://github.com/iiasa/ixmp/pull/115>`_: Support iterating with user-supplied callbacks.
-- `#130 <https://github.com/iiasa/ixmp/pull/130>`_: Recognize ``IXMP_DATA`` environment variable for configuration and local databases.
-- `#129 <https://github.com/iiasa/ixmp/pull/129>`_,
-  `#132 <https://github.com/iiasa/ixmp/pull/132>`_: Fully implement :meth:`~.Scenario.clone` across platforms (databases).
-- `#128 <https://github.com/iiasa/ixmp/pull/128>`_,
-  `#137 <https://github.com/iiasa/ixmp/pull/137>`_: New module :mod:`ixmp.testing` for reuse of testing utilities.
-- `#125 <https://github.com/iiasa/ixmp/pull/125>`_: Add functions to view and add regions for IAMC-style timeseries data.
-- `#123 <https://github.com/iiasa/ixmp/pull/123>`_: Return absolute path from ``find_dbprops()``.
-- `#118 <https://github.com/iiasa/ixmp/pull/118>`_: Switch to RTD Sphinx theme.
-- `#116 <https://github.com/iiasa/ixmp/pull/116>`_: Bugfix and extend functionality for working with IAMC-style timeseries data.
-- `#111 <https://github.com/iiasa/ixmp/pull/111>`_: Add functions to check if a Scenario has an item (set, par, var, equ).
-- `#110 <https://github.com/iiasa/ixmp/pull/110>`_: Generalize the internal functions to format index dimensions for mapping sets and parameters.
-- `#108 <https://github.com/iiasa/ixmp/pull/105>`_: Improve documentation.
-- `#105 <https://github.com/iiasa/ixmp/pull/105>`_: Replace `deprecated <http://pandas.pydata.org/pandas-docs/stable/indexing.html#ix-indexer-is-deprecated>`_ pandas ``.ix`` indexer with ``.iloc``.
-- `#103 <https://github.com/iiasa/ixmp/pull/103>`_: Specify dependencies in setup.py.
+- :pull:`135`: Test ``rixmp`` (former ``retixmp``) using the R ``testthat`` package.
+- :pull:`142`: Cloning across platforms, better support of IAMC_style timeseries data, preparations for MESSAGEix release 1.2 in Java core.
+- :pull:`115`: Support iterating with user-supplied callbacks.
+- :pull:`130`: Recognize ``IXMP_DATA`` environment variable for configuration and local databases.
+- :pull:`129`,
+  :pull:`132`: Fully implement :meth:`~.Scenario.clone` across platforms (databases).
+- :pull:`128`,
+  :pull:`137`: New module :mod:`ixmp.testing` for reuse of testing utilities.
+- :pull:`125`: Add functions to view and add regions for IAMC-style timeseries data.
+- :pull:`123`: Return absolute path from ``find_dbprops()``.
+- :pull:`118`: Switch to RTD Sphinx theme.
+- :pull:`116`: Bugfix and extend functionality for working with IAMC-style timeseries data.
+- :pull:`111`: Add functions to check if a Scenario has an item (set, par, var, equ).
+- :pull:`110`: Generalize the internal functions to format index dimensions for mapping sets and parameters.
+- :pull:`108`: Improve documentation.
+- :pull:`105`: Replace `deprecated <http://pandas.pydata.org/pandas-docs/stable/indexing.html#ix-indexer-is-deprecated>`_ pandas ``.ix`` indexer with ``.iloc``.
+- :pull:`103`: Specify dependencies in setup.py.
 
 v0.1.3 (2018-11-21)
 ===================
 
-- `#88 <https://github.com/iiasa/ixmp/pull/80>`_: Connecting to multiple databases, updating MESSAGE-scheme scenario specifications to version 1.1.
-- `#80 <https://github.com/iiasa/ixmp/pull/80>`_: Can now set logging level which is harmonized between Java and Python.
-- `#79 <https://github.com/iiasa/ixmp/pull/79>`_: Adding a deprecated-warning for `ixmp.Scenario` with `scheme=='MESSAGE'`.
-- `#76 <https://github.com/iiasa/ixmp/pull/76>`_: Changing the API from ``mp.Scenario(...)`` to ``ixmp.Scenario(mp, ...)``.
-- `#73 <https://github.com/iiasa/ixmp/pull/73>`_: Adding a function :meth:`~.Scenario.has_solution`, rename kwargs to `..._solution`.
-- `#69 <https://github.com/iiasa/ixmp/pull/69>`_: Bring retixmp available to other users.
-- `#64 <https://github.com/iiasa/ixmp/pull/64>`_: Support writing multiple sheets to Excel in utils.pd_write.
-- `#61 <https://github.com/iiasa/ixmp/pull/61>`_: Now able to connect to multiple databases (Platforms).
-- `#58 <https://github.com/iiasa/ixmp/pull/58>`_: Add MacOSX support in CI.
-- `#52 <https://github.com/iiasa/ixmp/pull/52>`_: Add ability to load all scenario data into memory for fast subsequent computation.
+- :pull:`88`: Connecting to multiple databases, updating MESSAGE-scheme scenario specifications to version 1.1.
+- :pull:`80`: Can now set logging level which is harmonized between Java and Python.
+- :pull:`79`: Adding a deprecated-warning for `ixmp.Scenario` with `scheme=='MESSAGE'`.
+- :pull:`76`: Changing the API from ``mp.Scenario(...)`` to ``ixmp.Scenario(mp, ...)``.
+- :pull:`73`: Adding a function :meth:`~.Scenario.has_solution`, rename kwargs to `..._solution`.
+- :pull:`69`: Bring retixmp available to other users.
+- :pull:`64`: Support writing multiple sheets to Excel in utils.pd_write.
+- :pull:`61`: Now able to connect to multiple databases (Platforms).
+- :pull:`58`: Add MacOSX support in CI.
+- :pull:`52`: Add ability to load all scenario data into memory for fast subsequent computation.

ci/Dockerfile

@@ -4,7 +4,7 @@ FROM openjdk:11-slim-buster
 ARG VIRTUAL_ENV=/opt/python3
 
 RUN apt-get update &&\
-    apt-get install -y --no-install-recommends curl gcc graphviz python3 \
+    apt-get install -y --no-install-recommends curl gcc git graphviz python3 \
       python3-dev python3-distlib python3-pip python3-setuptools python3-zmq \
       unzip &&\
     pip3 install virtualenv &&\

doc/README.rst

@@ -8,7 +8,7 @@ The documentation of the ix modeling platform is generated from .rst files in
 Dependencies
 ------------
 
-1. Sphinx_ v1.8 or higher
+1. Sphinx_ v3.0 or higher
 2. `sphinx_rtd_theme`
 3. `sphinxcontrib.bibtex`
 4. `numpydoc`