Merge branch 'enh/settings_set_use' into 'master'

Enh/settings set use

See merge request fsl/fslpy!66

.ci/build_conda_dist.sh

-#!/usr/bin/env bash
-
-set -e
-
-name=$1
-version=$2
-
-# add any extra channels that are needed
-for channel in $FSL_CONDA_CHANNELS; do
-    conda config  --append channels $channel
-done
-
-# make sure to update fundamental
-# packages from the default channel
-conda update  --yes -c defaults -n base conda
-conda install --yes -c defaults -n base setuptools conda-build
-
-# insert project name/version into meta.yaml
-echo "{% set name    = '$name' %}"    >  vars.txt
-echo "{% set version = '$version' %}" >> vars.txt
-cat vars.txt .conda/meta.yaml > tempfile
-mv tempfile .conda/meta.yaml
-rm vars.txt
-
-mkdir -p dist/conda-bld
-
-conda build --output-folder=dist/conda-bld .conda
-
-# Make sure package is installable
-for pyver in 2.7 3.4 3.5 3.6; do
-    conda create -y --name "test$pyver" python=$pyver
-    source activate test$pyver
-    conda install -y -c file://`pwd`/dist/conda-bld $name
-    source deactivate
-done

.ci/deploy_conda.sh

-#!/usr/bin/env bash
-
-set -e
-
-rsync -rv dist/conda-bld/ --exclude 'repodata*' --exclude "*json" "condadeploy:"
-ssh condaindex

.conda/conda_build_config.yaml

-python:
-   - 3.6
\ No newline at end of file

.conda/meta.yaml

-{% set data = load_setup_py_data() %}
-package:
-  name: fslpy
-  version: {{ data['version']}}
-
-build:
-  noarch: python
-  script: python setup.py install --single-version-externally-managed --record=record.txt
-
-source:
-  path: ../
-
-requirements:
-  build:
-    - python {{ python }}
-    - setuptools
-    {% for package in data.get('setup_requires', {}) %}
-    - {{ package.lower() }}
-    {% endfor %}
-
-  run:
-    - python
-    {% for package in data.get('install_requires', {}) %}
-    - {{ package.lower() }}
-    {% endfor %}
-
-  run_constrained:
-    {% for name, pkgs in data.get('extras_require', dict()).items() %}
-    {% for package in pkgs %}
-    - {{ package.lower() }}
-    {% endfor %}
-    {% endfor %}
-
-{% if 'test_suite' in data %}
-test:
-  requires:
-    {% for package in data.get('setup_requires', {}) %}
-    - {{ package.lower() }}
-    {% endfor %}
-  source_files:
-    - {{ data['test_suite'] }}
-  commands:
-    - python -m pytest {{ data['test_suite'] }} -m "not (fsltest or wxtest or dicomtest or meshtest or igziptest or noroottest or longtest)"
-{% endif %}
-
-about:
-  license_file: LICENSE

.conda/post-link.sh

-if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonLink.sh ]; then
-    $FSLDIR/etc/fslconf/requestFSLpythonLink.sh atlasquery atlasq imcp immv imglob extract_noise
-fi

.conda/pre-unlink.sh

-if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonUnlink.sh ]; then 
-    $FSLDIR/etc/fslconf/requestFSLpythonUnlink.sh atlasquery atlasq imcp immv imglob
-fi

.gitlab-ci.yml

@@ -11,7 +11,7 @@
 #
 #    3. doc:    Building API documentation
 #
-#    4. build:  Building source, wheel and conda distributions
+#    4. build:  Building source and wheel distributions
 #
 #    5. deploy: Uploading the build outputs to pypi/hosting servers, and the
 #               documentation to a hosting server.
@@ -64,12 +64,6 @@ stages:
 #   - SSH_PRIVATE_KEY_DOC_DEPLOY     - private key for rsyncing documentation
 #                                      to remote host (DOC_HOST)
 #
-#   - SSH_PRIVATE_KEY_CONDA_DEPLOY   - private key for rsyncing conda builds
-#                                      to remote host (CONDA_HOST)
-#
-#   - SSH_PRIVATE_KEY_CONDA_INDEX    - private key for updating conda channel
-#                                      (on CONDA_HOST)
-#
 #   - SSH_SERVER_HOSTKEYS            - List of trusted SSH hosts
 #
 #   - DOC_HOST:                      - Username@host to upload documentation to
@@ -78,12 +72,6 @@ stages:
 #   - FSL_HOST:                      - Username@host to download FSL data from
 #                                      (e.g. "paulmc@jalapeno.fmrib.ox.ac.uk")
 #
-#   - CONDA_HOST:                    - Username@host to upload conda build to
-#                                      (e.g. "paulmc@jalapeno.fmrib.ox.ac.uk")
-#
-#   - CONDA_CHANNELS                 - List of additional conda channels to
-#                                      use for conda build.
-#
 #   - TWINE_USERNAME:                - Username to use when uploading to pypi
 #
 #   - TWINE_PASSWORD:                - Password to use when uploading to pypi
@@ -244,25 +232,6 @@ build-pypi-dist:
       - dist/*
 
 
-build-conda-dist:
-  <<: *only_releases
-  <<: *patch_version
-
-  stage: build
-  image: continuumio/miniconda3
-
-  tags:
-    - docker
-
-  script:
-   - bash ./.ci/build_conda_dist.sh fslpy "$CI_COMMIT_REF_NAME"
-
-  artifacts:
-    expire_in: 1 day
-    paths:
-      - dist/conda-bld
-
-
 ##############
 # Deploy stage
 ##############
@@ -300,21 +269,3 @@ deploy-pypi:
 
   script:
     - bash ./.ci/deploy_pypi.sh
-
-
-
-deploy-conda:
-  <<: *only_releases
-  <<: *setup_ssh
-  stage: deploy
-  when:  manual
-  image: python:3.5
-
-  tags:
-    - docker
-
-  dependencies:
-    - build-conda-dist
-
-  script:
-    - bash ./.ci/deploy_conda.sh

AUTHOR

 Paul McCarthy <pauldmccarthy@gmail.com>
 Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
 Matthew Webster <matthew.webster@ndcn.ox.ac.uk>
-Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
\ No newline at end of file
+Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
+Martin Craig <martin.craig@eng.ox.ac.uk>
\ No newline at end of file

CHANGELOG.rst

@@ -2,6 +2,26 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+1.11.0 (Thursday September 13th 2018)
+-------------------------------------
+
+
+Added
+^^^^^
+
+
+* A couple of new convenience functions to the :mod:`.settings` module.
+
+
+Changed
+^^^^^^^
+
+
+* Development (test and documentation dependencies) are no longer listed
+  in ``setup.py`` - they now need to be installed manually.
+* Removed conda build infrastructure.
+
+
 1.10.3 (Sunday September 9th 2018)
 ----------------------------------
 

README.rst

@@ -11,6 +11,9 @@ fslpy
 .. image:: https://img.shields.io/pypi/v/fslpy.svg
    :target: https://pypi.python.org/pypi/fslpy/
 
+.. image:: https://anaconda.org/conda-forge/fslpy/badges/version.svg
+   :target: https://anaconda.org/conda-forge/fslpy
+
 
 The ``fslpy`` project is a `FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_
 programming library written in Python. It is used by `FSLeyes
@@ -26,6 +29,11 @@ Install ``fslpy`` and its core dependencies via pip::
     pip install fslpy
 
 
+``fslpy`` is also available on `conda-forge <https://conda-forge.org/>`_::
+
+    conda install -c conda-forge fslpy
+
+
 Dependencies
 ------------
 
@@ -36,16 +44,16 @@ All of the core dependencies of ``fslpy`` are listed in the `requirements.txt
 Some extra dependencies are listed in `requirements.txt
 <requirements-extra.txt>`_ which provide addditional functionality:
 
- - ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
-   functionality  to schedule functions on the ``wx`` idle loop.
+- ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
+  functionality  to schedule functions on the ``wx`` idle loop.
 
- - ``indexed_gzip``: The `fsl.data.image.Image <fsl/data/image.py>`_ class
-   can use ``indexed_gzip`` to keep large compressed images on disk instead
-   of decompressing and loading them into memory..
+- ``indexed_gzip``: The `fsl.data.image.Image <fsl/data/image.py>`_ class
+  can use ``indexed_gzip`` to keep large compressed images on disk instead
+  of decompressing and loading them into memory..
 
- - ``trimesh``/``rtree``: The `fsl.data.mesh.TriangleMesh <fsl/data/mesh.py>`_
-   class has some methods which use ``trimesh`` to perform geometric queries
-   on the mesh.
+- ``trimesh``/``rtree``: The `fsl.data.mesh.TriangleMesh <fsl/data/mesh.py>`_
+  class has some methods which use ``trimesh`` to perform geometric queries
+  on the mesh.
 
 
 If you are using Linux, need to install wxPython first, as binaries are not
@@ -64,33 +72,43 @@ the rest of the extra dependencies::
     pip install fslpy[extras]
 
 
+Dependencies for testing and documentation are listed in the
+`requirements-dev.txt <requirements-dev.txt>`_ file.
+
+
 Documentation
 -------------
 
 ``fslpy`` is documented using `sphinx <http://http://sphinx-doc.org/>`_. You
 can build the API documentation by running::
 
+    pip install -r requirements-dev.txt
     python setup.py doc
 
 The HTML documentation will be generated and saved in the ``doc/html/``
 directory.
 
 
-If you are interested in contributing to ``fslpy``, check out the
-`contributing guide <doc/contributing.rst>`_.
-
-
 Tests
 -----
 
 Run the test suite via::
 
+    pip install -r requirements-dev.txt
     python setup.py test
 
 A test report will be generated at ``report.html``, and a code coverage report
 will be generated in ``htmlcov/``.
 
 
+Contributing
+------------
+
+
+If you are interested in contributing to ``fslpy``, check out the
+`contributing guide <doc/contributing.rst>`_.
+
+
 Credits
 -------
 

fsl/utils/settings.py

@@ -25,6 +25,16 @@ the following functions can be called at the module-level:
    Settings.clear
 
 
+Some functions are also available to replace the module-level :class:`Settings`
+instance:
+
+.. autosummary::
+   :nosignatures:
+
+   set
+   use
+
+
 These functions will have no effect before :func:`initialise` is called.
 
 Two types of configuration data are available:
@@ -67,15 +77,9 @@ storing configuration files.
 """
 
 
-def initialise(*args, **kwargs):
-    """Initialise the ``settings`` module. This function creates a
-    :class:`Settings` instance, and enables the module-level
-    functions. All settings are passed through to :meth:`Settings.__init__`.
-    """
-
-    mod = sys.modules[__name__]
-
-    settings       = Settings(*args, **kwargs)
+def set(settings):
+    """Set the module-level :class:`Settings` instance. """
+    mod            = sys.modules[__name__]
     mod.settings   = settings
     mod.read       = settings.read
     mod.write      = settings.write
@@ -89,6 +93,31 @@ def initialise(*args, **kwargs):
     mod.clear      = settings.clear
 
 
+def initialise(*args, **kwargs):
+    """Initialise the ``settings`` module. This function creates a
+    :class:`Settings` instance, and enables the module-level
+    functions. All settings are passed through to :meth:`Settings.__init__`.
+    """
+    set(Settings(*args, **kwargs))
+
+
+@contextlib.contextmanager
+def use(settings):
+    """Temporarily replace the module-level :class:`Settings` object
+    with the given one.
+    """
+
+    mod = sys.modules[__name__]
+    old = getattr(mod, 'settings', None)
+
+    try:
+        set(settings)
+        yield
+    finally:
+        if old is not None:
+            set(old)
+
+
 # These are all overwritten by
 # the initialise function.
 def read(name, default=None):
@@ -391,7 +420,7 @@ class Settings(object):
         try:
             with open(configFile, 'wb') as f:
                 pickle.dump(config, f, protocol=2)
-        except (IOError, pickle.PicklingError, EOFError):
+        except (FileNotFoundError, IOError, pickle.PicklingError, EOFError):
             log.warning('Unable to save {} configuration file '
                         '{}'.format(self.__configID, configFile),
                         exc_info=True)

setup.py

@@ -23,10 +23,6 @@ basedir = op.dirname(__file__)
 with open(op.join(basedir, 'requirements.txt'), 'rt') as f:
     install_requires = [l.strip() for l in f.readlines()]
 
-# Development/test dependencies are listed in requirements-dev.txt
-with open(op.join(basedir, 'requirements-dev.txt'), 'rt') as f:
-    dev_requires = [l.strip() for l in f.readlines()]
-
 # Optional dependencies are listed in requirements-extra.txt
 with open(op.join(basedir, 'requirements-extra.txt'), 'rt') as f:
     extra_requires = {'extras' : [l.strip() for l in f.readlines()]}
@@ -116,7 +112,6 @@ setup(
 
     install_requires=install_requires,
     extras_require=extra_requires,
-    setup_requires=dev_requires,
 
     test_suite='tests',
 

tests/test_settings.py

@@ -23,6 +23,7 @@ import pytest
 
 import tests
 import fsl.utils.settings as settings
+import fsl.utils.tempdir  as tempdir
 
 
 def test_initialise():
@@ -431,3 +432,88 @@ def test_writeConfigFile():
         with open(op.join(testdir, 'config.pkl'), 'rb') as f:
             readback = pickle.load(f)
             assert testdata == readback
+
+
+
+def test_set():
+
+    with tempdir.tempdir(changeto=False) as td1,\
+         tempdir.tempdir(changeto=False) as td2:
+
+        s1 = settings.Settings(cfgdir=td1, writeOnExit=False)
+        s2 = settings.Settings(cfgdir=td2, writeOnExit=False)
+
+        settings.set(s1)
+        with settings.writeFile('file1') as f:
+            f.write('hi!')
+        assert os.listdir(td1) == ['file1']
+        assert os.listdir(td2) == []
+
+        settings.set(s2)
+        with settings.writeFile('file2') as f:
+            f.write('hi!')
+        assert os.listdir(td1) == ['file1']
+        assert os.listdir(td2) == ['file2']
+
+        settings.set(s1)
+        with settings.writeFile('file3') as f:
+            f.write('hi!')
+        assert sorted(os.listdir(td1)) == ['file1', 'file3']
+        assert        os.listdir(td2)  == ['file2']
+
+        settings.set(s2)
+        with settings.writeFile('file4') as f:
+            f.write('hi!')
+        assert sorted(os.listdir(td1)) == ['file1', 'file3']
+        assert sorted(os.listdir(td2)) == ['file2', 'file4']
+
+
+def test_use():
+
+    with tempdir.tempdir(changeto=False) as td1,\
+         tempdir.tempdir(changeto=False) as td2:
+
+        s1 = settings.Settings(cfgdir=td1, writeOnExit=False)
+        s2 = settings.Settings(cfgdir=td2, writeOnExit=False)
+
+        with settings.use(s1):
+            with settings.writeFile('file1') as f:
+                f.write('hi!')
+
+        assert os.listdir(td1) == ['file1']
+        assert os.listdir(td2) == []
+
+        with settings.use(s2):
+            with settings.writeFile('file2') as f:
+                f.write('hi!')
+
+        settings.set(s1)
+        with settings.writeFile('file3') as f:
+                f.write('hi!')
+
+        with settings.use(s2):
+            with settings.writeFile('file4') as f:
+                f.write('hi!')
+
+        assert sorted(os.listdir(td1)) == ['file1', 'file3']
+        assert sorted(os.listdir(td2)) == ['file2', 'file4']
+
+        # should go back to s1
+        with settings.writeFile('file5') as f:
+            f.write('hi!')
+
+        assert sorted(os.listdir(td1)) == ['file1', 'file3', 'file5']
+        assert sorted(os.listdir(td2)) == ['file2', 'file4']
+
+        try:
+            with settings.use(s2):
+                raise Exception('hur')
+        except Exception:
+            pass
+
+        # should go back to s1
+        with settings.writeFile('file6') as f:
+            f.write('hi!')
+
+        assert sorted(os.listdir(td1)) == ['file1', 'file3', 'file5', 'file6']
+        assert sorted(os.listdir(td2)) == ['file2', 'file4']