Merge pull request #305 from EducationalTestingService/update-conda-r…

…ecipe

Update conda recipe and requirements

.travis.yml

@@ -12,7 +12,7 @@ env:
   matrix:
   - TESTFILES="tests/test_experiment_rsmtool_1.py"
   - TESTFILES="tests/test_comparer.py tests/test_configuration_parser.py tests/test_experiment_rsmtool_2.py"
-  - TESTFILES="tests/test_analyzer.py tests/test_experiment_rsmeval.py tests/test_fairness_utils.py tests/test_prmse_utils.py"
+  - TESTFILES="tests/test_analyzer.py tests/test_experiment_rsmeval.py tests/test_fairness_utils.py tests/test_prmse_utils.py tests/test_container.py"
   - TESTFILES="tests/test_experiment_rsmcompare.py tests/test_experiment_rsmsummarize.py tests/test_modeler.py tests/test_preprocessor.py tests/test_writer.py tests/test_experiment_rsmtool_3.py"
   - TESTFILES="tests/test_experiment_rsmpredict.py tests/test_reader.py tests/test_reporter.py tests/test_transformer.py tests/test_utils.py tests/test_experiment_rsmtool_4.py"
 sudo: false
@@ -21,10 +21,10 @@ before_install:
 - if [ -x ${HOME}/miniconda3/pkgs ]; then pushd ${HOME}/miniconda3/pkgs && find -maxdepth 1 -mindepth 1 -type d | xargs rm -rf && popd; fi
 - chmod +x miniconda.sh
 - ./miniconda.sh -b -f
-- ${HOME}/miniconda3/bin/conda update --yes conda
+- ${HOME}/miniconda3/bin/conda install -c anaconda --yes setuptools
 
 install:
-- ${HOME}/miniconda3/bin/conda create --name rsmenv -c defaults -c conda-forge -c desilinguist --file conda_requirements.txt --yes --quiet
+- ${HOME}/miniconda3/bin/conda create --name rsmenv -c defaults -c conda-forge -c desilinguist --file requirements.txt --yes --quiet
 - ${HOME}/miniconda3/envs/rsmenv/bin/pip install nose-cov python-coveralls
 - ${HOME}/miniconda3/envs/rsmenv/bin/pip install -e .
 

DistributeTests.ps1

@@ -35,6 +35,7 @@ elseif ($agentNumber -eq 2) {
     $testsToRun = $testsToRun + "tests/test_comparer.py"
     $testsToRun = $testsToRun + "tests/test_configuration_parser.py"
     $testsToRun = $testsToRun + "tests/test_experiment_rsmtool_2.py"
+    $testsToRun = $testsToRun + "tests/test_container.py"
 }
 elseif ($agentNumber -eq 3) {
     $testsToRun = $testsToRun + "tests/test_analyzer.py"

MANIFEST.in

@@ -1,8 +1,11 @@
 include LICENSE
 include *.rst
 include requirements.txt
+recursive-exclude doc *
+recursive-exclude tests *
+recursive-exclude examples *
 recursive-include rsmtool/notebooks *
-recursive-include doc *
 prune test_outputs
+prune rsmtool/rsmtool.egg-info
 prune rsmtool/notebooks/.ipynb_checkpoints
 prune rsmtool/notebooks/comparison/.ipynb_checkpoints

conda-recipe/rsmtool/meta.yaml

@@ -1,15 +1,18 @@
+{% set data = load_setup_py_data() %}
+
 package:
   name: rsmtool
-  version: 6.1.0
+  version: {{data.get('version')}}
 
 source:
   path: ../../../rsmtool
 
 build:
   number: 0
+  noarch: python
   script:
     - cd $SRC_DIR
-    - $PYTHON setup.py install
+    - "{{ PYTHON }} -m pip install . --no-deps -vv"
   entry_points:
     - rsmtool = rsmtool.rsmtool:main
     - rsmcompare = rsmtool.rsmcompare:main
@@ -19,55 +22,19 @@ build:
     - render_notebook = rsmtool.reporter:main
     - convert_feature_json = rsmtool.convert_feature_json:main
 
+{% block requirements -%}
 requirements:
   build:
-    - python
-    - numpy>=1.14.0,<1.15
-    - scipy>=1.1.0,<1.2.0
-    - ipython>=6.5.0,<6.5.1
-    - jupyter>=1.0.0,<1.1
-    - joblib>=0.11,<0.12
-    - matplotlib>=2.1.2,<2.2
-    - nose>=1.3.7,<1.4
-    - notebook>=5.7.2,<5.8
-    - pandas>=0.23.4,<0.23.5
-    - scikit-learn>=0.19.1,<0.19.2
-    - seaborn>=0.9.0,<0.10.0
-    - skll>=1.5,<1.6
-    - statsmodels>=0.9.0,<0.9.1
-    - sphinx
-    - sphinx_rtd_theme
-    - zeromq
-    - coverage
-    - parameterized
-    - setuptools
-    - openpyxl
-    - xlrd
-    - xlwt
-
+    - python >=3.6
+    {% for req in data.get('install_requires', []) -%}
+    - {{req.replace(">", " >").replace("<", " <").replace("==", " ")}}
+    {% endfor %}
   run:
-    - python
-    - numpy>=1.14.0,<1.15
-    - scipy>=1.1.0,<1.2.0
-    - ipython>=6.5.0,<6.5.1
-    - jupyter>=1.0.0,<1.1
-    - joblib>=0.11,<0.12
-    - matplotlib>=2.1.2,<2.2
-    - nose>=1.3.7,<1.4
-    - notebook>=5.7.2,<5.8
-    - pandas>=0.23.4,<0.23.5
-    - scikit-learn>=0.19.1,<0.19.2
-    - seaborn>=0.9.0,<0.10.0
-    - skll>=1.5,<1.6
-    - statsmodels>=0.9.0,<0.9.1
-    - sphinx
-    - sphinx_rtd_theme
-    - zeromq
-    - coverage
-    - parameterized
-    - openpyxl
-    - xlrd
-    - xlwt
+    - python >=3.6
+    {% for req in data.get('install_requires', []) -%}
+    - {{req.replace(">", " >").replace("<", " <").replace("==", " ")}}
+    {% endfor %}
+{%- endblock %}
 
 test:
   # Python imports
@@ -99,3 +66,4 @@ test:
 about:
   home: https://github.com/EducationalTestingService/rsmtool
   license: Apache 2.0
+  license_file: LICENSE

doc/contributing.rst

@@ -12,9 +12,9 @@ To set up a local development environment, follow the steps below:
 
 2. If you already have the ``conda`` package manager installed, skip to the next step. If you do not, follow the instructions on `this page <https://conda.io/docs/user-guide/install/index.html>`_ to install conda.
 
-3. Create a new conda environment (say, ``rsmtool``) and install the packages specified in the ``conda_requirements.txt`` file by running::
+3. Create a new conda environment (say, ``rsmtool``) and install the packages specified in the ``requirements.txt`` file by running::
 
-    conda create -n rsmtool -c defaults -c conda-forge -c desilinguist --file conda_requirements.txt
+    conda create -n rsmtool -c defaults -c conda-forge -c desilinguist --file requirements.txt
 
 4. Activate the environment using ``source activate rsmtool`` (use ``activate rsmtool`` if you are on Windows).
 

environment.yml

@@ -3,26 +3,23 @@ channels:
   - conda-forge
   - desilinguist
 dependencies:
-- python==3.6.3
-- ipython=6.3.1
-- jupyter=1.0.0
-- joblib=0.11
-- matplotlib=2.1.2
-- nose=1.3.7
-- notebook=5.4.1
-- numpy=1.13.3
-- pandas=0.22.0
-- scikit-learn=0.19.1
-- scipy=1.0.0
-- seaborn=0.9.0
-- skll=1.5.2
-- statsmodels=0.9.0
-- parameterized
-- zeromq
-- sphinx
-- sphinx_rtd_theme
-- coverage
-- setuptools
-- openpyxl
-- xlrd
-- xlwt
+  - python
+  - ipython=6.5.0
+  - jupyter=1.0.0
+  - joblib=0.11
+  - matplotlib=2.1.2
+  - nose=1.3.7
+  - notebook=5.7.2
+  - numpy
+  - pandas
+  - scipy
+  - seaborn
+  - skll=1.5.2
+  - statsmodels
+  - coverage
+  - openpyxl
+  - parameterized
+  - sphinx
+  - sphinx_rtd_theme
+  - xlrd
+  - xlwt

requirements.txt

@@ -1,21 +1,15 @@
-ipython==6.5.0
-jupyter==1.0.0
-joblib==0.11
-matplotlib==2.1.2
-nose==1.3.7
-notebook==5.7.2
-numpy==1.14.*
+jupyter
+nose
+notebook
+numpy==1.14.6
 pandas==0.23.4
-scikit-learn==0.19.1
-scipy==1.1.0
-seaborn==0.9.0
+seaborn
 skll==1.5.2
-statsmodels==0.9.0
+statsmodels
+coverage
 openpyxl
-xlrd
-xlwt
+parameterized
 sphinx
 sphinx_rtd_theme
-coverage
-parameterized
-setuptools
+xlrd
+xlwt

rsmtool/notebooks/feature_descriptives.ipynb

@@ -84,12 +84,11 @@
     "    legend.legendHandles[0].set_color(colors[0])\n",
     "    legend.legendHandles[1].set_color(colors[1])\n",
     "\n",
-    "    # we want to try to force `tight_layout()`, but if this fails\n",
-    "    # we don't want the entire notebook to fail\n",
-    "    try:\n",
+    "    # we want to try to force `tight_layout()`, but if this \n",
+    "    # raises a warning, we don't want the entire notebook to fail\n",
+    "    with warnings.catch_warnings():\n",
+    "        warnings.simplefilter('ignore')\n",
     "        plt.tight_layout(h_pad=1.0)\n",
-    "    except ValueError:\n",
-    "        pass\n",
     "\n",
     "    imgfile = join(figure_dir, '{}_outliers.svg'.format(experiment_id))\n",
     "    plt.savefig(imgfile)\n",

rsmtool/notebooks/preprocessed_features.ipynb

@@ -56,7 +56,12 @@
     "            ax.set_xticklabels(labels, rotation=90)\n",
     "            ax.set_title(cname)\n",
     "\n",
-    "        plt.tight_layout(h_pad=1.0)\n",
+    "        # we want to try to force `tight_layout()`, but if this \n",
+    "        # raises a warning, we don't want the entire notebook to fail\n",
+    "        with warnings.catch_warnings():\n",
+    "            warnings.simplefilter('ignore')\n",
+    "            plt.tight_layout(h_pad=1.0)\n",
+    "\n",
     "        imgfile = join(figure_dir, '{}_distrib.svg'.format(experiment_id))\n",
     "        plt.savefig(imgfile)\n",
     "        if use_thumbnails:\n",

rsmtool/version.py

@@ -3,5 +3,5 @@
 in one place. Based on the suggestion `here. <http://bit.ly/16LbuJF>`_
 """
 
-__version__ = '6.1.0'
+__version__ = '7.0.0'
 VERSION = tuple(int(x) for x in __version__.split('.'))