Merge pull request #416 from iiasa/issue/415

Improve testing for v3.3; misc cleanup

.github/workflows/pytest.yaml

@@ -99,41 +99,25 @@ jobs:
     - name: Install Python package and dependencies
       run: pip install .[tests]
 
-    - name: Install R package and dependencies
+    - name: Install R dependencies and tutorial requirements
       run: |
         install.packages("remotes")
-        remotes::install_cran(c("rcmdcheck", "IRkernel"))
-        remotes::install_deps("rixmp", upgrade = "never", dependencies = TRUE)
+        remotes::install_cran(
+          c("IRkernel", "reticulate"),
+          dependencies = TRUE,
+          # force = TRUE,
+        )
+
+        IRkernel::installspec()
 
         # commented: for debugging
         # print(reticulate::py_config())
         # reticulate::py_run_string("import os; print(os.environ)")
-
-        # For R tutorial notebooks, run via the pytest suite: set up R kernel;
-        # actually install the R package
-        IRkernel::installspec()
-        remotes::install_local(
-          "rixmp",
-          force = TRUE,
-          INSTALL_opts = c("--no-multiarch"),
-          )
       shell: Rscript {0}
 
     - name: Run test suite using pytest
       run: pytest ixmp -m "not performance" --verbose -rA --cov-report=xml --color=yes
 
-    - name: Run R CMD check
-      # Temporarily disabled: see https://github.com/iiasa/ixmp/issues/403
-      if: false
-      run: |
-        rcmdcheck::rcmdcheck(
-            "rixmp",
-            args = c("--no-manual", "--as-cran", "--no-multiarch"),
-            error_on = "warning",
-            check_dir = "check"
-        )
-      shell: Rscript {0}
-
     - name: Test documentation build using Sphinx
       if: matrix.python-version != '3.6'
       run: make --directory=doc html

.gitignore

@@ -55,6 +55,7 @@ rixmp/source/inst/docum/*.html
 *.pid
 coverage.xml
 htmlcov
+prof/
 
 # JetBrains IDEs
 *.iml

RELEASE_NOTES.rst

@@ -1,15 +1,24 @@
+.. _v3.3.0:
+
 Next release
 ============
 
 All changes
 -----------
 
+- :pull:`416`:
+
+  - Add ``ixmp config show`` CLI command.
+  - Add :mod:`genno` and :mod:`message_ix_models` to the output of :func:`show_versions` / ``ixmp show-versions``.
+  - Clean up test suite, improve performance, increase coverage ().
+
 - Deprecate :func:`.utils.logger` (:pull:`399`).
 - Add a `quiet` option to :meth:`.GAMSModel.solve` and use in testing (:pull:`399`).
 - :pull:`398`:
 
   - Fix :class:`.GAMSModel` would try to write GDX data to filenames containing invalid characters on Windows.
   - Format user-friendly exceptions when GAMSModel errors (:issue:`383`).
+
 - :pull:`397`: Adjust :mod:`ixmp.reporting` to use :mod:`genno`.
 - :pull:`396`: Fix two minor bugs in reporting.
 

doc/api-backend.rst

@@ -121,6 +121,7 @@ Backend API
       get_scenarios
       get_scenario_names
       get_units
+      handle_config
       open_db
       read_file
       remove_meta

doc/api-r.rst

@@ -1,39 +1,30 @@
 .. _rixmp:
 
-R (``rixmp`` package)
-*********************
+Usage in R via ``reticulate``
+*****************************
 
-An R interface to the `ixmp` is provided by the ``rixmp`` package.
-``rixmp`` uses the `reticulate <https://rstudio.github.io/reticulate/>`_ R-to-Python adapter to provide access to all features of the :mod:`ixmp` *Python* package
+:mod:`ixmp` is fully usable in R via `reticulate`_, a package that allows nearly seamless access to the Python API.
+No additional R packages are needed.
 
-.. code-block:: R
-
-   # Load the rixmp package
-   library(rixmp)
-   ixmp <- import('ixmp')
-
-   # An 'ixmp' object is added to the global namespace.
-   # It can be used in the same way as the Python ixmp package.
-   mp <- ixmp$Platform(dbtype = 'HSQLDB')
-   scen <- ixmp$Scenario(mp, 'model name', 'scenario name', version = 'new')
+.. note:: The former ``rixmp`` package was removed in :mod:`ixmp` :ref:`v3.3.0`.
 
-   # etc.
+See :ref:`message_ix:install-r` for installing R and `reticulate`_ to use with :mod:`ixmp`.
+Those instructions are suitable whether :mod:`message_ix` is also installed, or only :mod:`ixmp`.
 
-One additional method, :meth:`adapt_to_ret` is provided.
-Access its documentation with
+Once installed, use reticulate to import the Python package:
 
 .. code-block:: R
 
-   ?rixmp::adapt_to_ret
+   library(reticulate)
+   ixmp <- import("ixmp")
 
-This function is useful when adding :class:`data.frames` objects to a Scenario:
+This creates a global variable, ``ixmp``, that can be used much like the Python module:
 
 .. code-block:: R
 
-   scen$init_set("i")
-   i.set = c("seattle", "san-diego")
-   scen$add_set("i", i.set)
-   # load dataframes
-   scen$init_par("a", c("i"))
-   a.df = data.frame(i = i.set, value = c(350, 600) , unit = 'cases')
-   scen$add_par("a", adapt_to_ret(a.df))
+   mp <- ixmp$Platform(name = 'default')
+   scen <- ixmp$Scenario(mp, 'model name', 'scenario name', version = 'new')
+
+Finally, see the R versions of the :doc:`tutorials`.
+
+.. _reticulate: https://rstudio.github.io/reticulate/

doc/file-io.rst

@@ -84,4 +84,4 @@ Multiple dimensions indexed by the same set
 File formats other than :file:`.xlsx`
    The :file:`.xlsx` (Office Open XML) file format is preferred for input and output.
    :mod:`ixmp` uses `openpyxl <https://openpyxl.readthedocs.io>`_ and :mod:`pandas` in order to read and write this format.
-   For other Excel file formats, including :file:`.xls` and :file:`.xlsb`, see the :pandas:ref:`Pandas documentation <io.excel>`.
+   For other Excel file formats, including :file:`.xls` and :file:`.xlsb`, see the :ref:`Pandas documentation <pandas:io.excel>`.

doc/install.rst

@@ -7,6 +7,8 @@ The sections below cover other use cases.
 Ensure you have first read the :doc:`prerequisites <prereqs>` for understanding and using |MESSAGEix|.
 These include specific points of knowledge that are necessary to understand these instructions and choose among different installation options.
 
+To use :mod:`ixmp` from R, see :ref:`message_ix:install-r` in the |MESSAGEix| documentation.
+
 Use cases for installing ixmp directly include:
 
 - Installing *ixmp* to be used alone (i.e., with models or frameworks other than |MESSAGEix|).
@@ -21,13 +23,6 @@ Use cases for installing ixmp directly include:
   - `Install system dependencies`_, then
   - `From source`_.
 
-- Installing the :doc:`rixmp <api-r>` R package, to use the :mod:`ixmp`, alone, from R.
-  Again, to use |MESSAGEix| from R, it is sufficient to install ``rmessageix``; and not necessary to also/separately install ``rximp``.
-
-  - Start with `Install system dependencies`_.
-  - Then install :mod:`ixmp` from source.
-  - Finally, see `Install rixmp`_.
-
 **Contents:**
 
 .. contents::
@@ -123,7 +118,7 @@ From source
 
 4. (Optional) If you intend to contribute changes to *ixmp*, first register a Github account, and fork the `ixmp repository <https://github.com/iiasa/ixmp>`_.
    This will create a new repository ``<user>/ixmp``.
-   (Please also see :message_ix:doc:`contributing`.)
+   (Please also see :doc:`message_ix:contributing`.)
 
 5. Clone either the main repository, or your fork; using the `Github Desktop`_ client, or the command line::
 
@@ -144,42 +139,6 @@ From source
     $ pytest
 
 
-Install ``rixmp``
-=================
-
-``rixmp`` is the R interface to :mod:`ixmp`; see :doc:`its documentaiton <api-r>`.
-You only need to install ``rixmp`` if you intend to use :mod:`ixmp` from R, rather than from Python.
-
-Install :mod:`ixmp` **from source**, per the section above.
-Then:
-
-8. `Install R <https://www.r-project.org>`_.
-   Ensure that your ``PATH`` environment variable is configured correctly so that the ``Rscript`` executable is available.
-
-   .. warning::
-      Ensure the the R version installed is either 32- *or* 64-bit (and >= 3.5.0), consistently with GAMS and Java.
-      Having both 32- and 64-bit versions of R, or mixed 32- and 64-bit versions of different packages, can cause errors.
-
-9. Open a command prompt in the :file:`ixmp/` directory.
-   Type the following commands to build, then install, ``rixmp`` and its dependencies, including reticulate_::
-
-    $ R CMD build rixmp
-
-10. Check that there is only one :file:`*.tar.gz` or :file:`.zip` file in the folder, then run::
-
-      # On Windows
-      $ R CMD INSTALL rixmp_*.zip
-
-      # Other operating systems
-      $ R CMD INSTALL rixmp_*.tar.gz
-
-11. (Optional) Install `IRKernel`_, which allows running R code in Jupyter notebooks (see the link for instructions).
-
-12. (Optional) Check that the R interface works by using the built-in test suite to run the R tutorial notebooks::
-
-    $ pytest -m rixmp
-
-
 Troubleshooting
 ===============
 
@@ -216,12 +175,6 @@ Java Development Kit (JDK)
 
      .. warning:: Do not overwrite the existing ``PATH`` environment variable, but add to the list of existing paths.
 
-Rtools
-   https://cran.r-project.org/bin/windows/Rtools/
-
-   For installing or modifying some R packages on Windows.
-
-
 .. _`installing MESSAGEix`: https://docs.messageix.org/en/latest/getting_started.html
 .. _`Anaconda`: https://www.continuum.io/downloads
 .. _`GAMS`: http://www.gams.com
@@ -234,6 +187,4 @@ Rtools
 .. _conda glossary: https://docs.conda.io/projects/conda/en/latest/glossary.html
 .. _Anaconda Navigator documentation: https://docs.anaconda.com/anaconda/navigator/
 .. _`Github Desktop`: https://desktop.github.com
-.. _reticulate: https://rstudio.github.io/reticulate/
-.. _IRkernel: https://irkernel.github.io/installation/
 .. _JDK website instructions: https://docs.oracle.com/cd/E19182-01/820-7851/inst_cli_jdk_javahome_t/

ixmp/__init__.py

@@ -28,7 +28,7 @@
 
 try:
     __version__ = get_distribution(__name__).version
-except DistributionNotFound:
+except DistributionNotFound:  # pragma: no cover
     # Package is not installed
     __version__ = "999"