[med-svn] [Git][med-team/intake][upstream] New upstream version 0.6.4
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Oct 16 16:59:46 BST 2021
Étienne Mollier pushed to branch upstream at Debian Med / intake
Commits:
52f4106d by Étienne Mollier at 2021-10-16T17:00:31+02:00
New upstream version 0.6.4
- - - - -
9 changed files:
- .github/workflows/main.yaml
- MANIFEST.in
- docs/source/plugin-directory.rst
- docs/source/transforms.rst
- intake/_version.py
- intake/catalog/remote.py
- intake/interface/server.py
- intake/source/derived.py
- intake/tests/test_config.py
Changes:
=====================================
.github/workflows/main.yaml
=====================================
@@ -31,7 +31,7 @@ jobs:
- name: pip-install
shell: bash -l {0}
run: |
- pip install -e . --no-deps
+ pip install . --no-deps
- name: Run Tests
shell: bash -l {0}
=====================================
MANIFEST.in
=====================================
@@ -5,15 +5,17 @@ recursive-include intake *.yml
recursive-include intake *.yaml
recursive-include intake *.zip
recursive-include intake *.png
-recursive-include intake/source/tests/plugin_searchpath *.py
-recursive-include intake/catalog/tests/catalog_search *
-recursive-include docs/source *
-include docs/Makefile docs/make.bat
-
recursive-include templates *
include versioneer.py
include intake/_version.py
-include intake/catalog/tests/example_plugin_dir/example2_source.py
include requirements.txt
+include setup.py
include LICENSE
+include intake/cli/sample/*
+
+prune **/tests/**
+prune docs
+recursive-include intake/source/tests/plugin_searchpath *.py
+recursive-include intake/catalog/tests/catalog_search *
+
=====================================
docs/source/plugin-directory.rst
=====================================
@@ -26,6 +26,7 @@ contains in parentheses:
* `intake-notebook <https://github.com/informatics-lab/intake-notebook>`_: Experimental plugin to access parameterised notebooks through intake and executed via papermill (``ipynb``)
* `intake-odbc <https://github.com/intake/intake-odbc>`_: ODBC database (``odbc``)
* `intake-parquet <https://github.com/intake/intake-parquet>`_: Apache Parquet file format (``parquet``)
+* `intake-pattern-catalog <https://bitbucket.org/dtnse/intake_pattern_catalog/>`_: Plugin for specifying a file-path pattern which can represent a number of different entries (``pattern_cat``)
* `intake-pcap <https://github.com/intake/intake-pcap>`_: PCAP network packet format (``pcap``)
* `intake-postgres <https://github.com/intake/intake-postgres>`_: PostgreSQL database (``postgres``)
* `intake-s3-manifests <https://github.com/informatics-lab/intake-s3-manifests>`_ (``s3_manifest``)
=====================================
docs/source/transforms.rst
=====================================
@@ -81,7 +81,7 @@ applies a column selection to it.
Running ``cat.derive_cols.read()`` will indeed, as expected, produce a version of the data
with only the selected columns included. It does this by defining the original dataset,
-appying the selection, and then getting Dask to generate the output. For some datastets,
+appying the selection, and then getting Dask to generate the output. For some datasets,
this can mean that the selection is pushed down to the reader, and the data for the dropped
columns is never loaded. The user may choose to do ``.to_dask()`` instead, and manipulate
the lazy dataframe directly, before loading.
@@ -151,7 +151,7 @@ Execution engine
None of the above example specified explicitly where the compute implied by the
transformation will take place. However, most Intake drivers support in-memory containers
-and Dask; remembering that the input dataste here is a dataframe. However, the behaviour
+and Dask; remembering that the input dataset here is a dataframe. However, the behaviour
is defined in the driver class itself - so it would be fine to write a driver in which
we make different assumptions. Let's suppose, for instance, that the original source
is to be loaded from ``spark`` (see the ``intake-spark`` package), the driver could
=====================================
intake/_version.py
=====================================
@@ -24,9 +24,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 0.6.3)"
- git_full = "8203c966cf90732be5fcb9c37a504a398a21223d"
- git_date = "2021-08-09 09:33:32 -0400"
+ git_refnames = " (HEAD -> master, tag: 0.6.4)"
+ git_full = "d9faa048bbc09d74bb6972f672155e3814c3ca62"
+ git_date = "2021-10-08 10:34:28 -0400"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
intake/catalog/remote.py
=====================================
@@ -32,7 +32,7 @@ class RemoteCatalog(Catalog):
def __init__(self, url, http_args=None, page_size=None,
name=None, source_id=None, metadata=None, auth=None, ttl=1,
getenv=True, getshell=True,
- storage_options=None, parameters=None):
+ storage_options=None, parameters=None, persist_mode="default"):
"""Connect to remote Intake Server as a catalog
Parameters
@@ -97,7 +97,7 @@ class RemoteCatalog(Catalog):
'.', '_').replace(':', '_')
super(RemoteCatalog, self).__init__(
name=name, metadata=name, ttl=ttl, getenv=getenv,
- getshell=getshell, storage_options=storage_options)
+ getshell=getshell, storage_options=storage_options, persist_mode=persist_mode)
def _make_entries_container(self):
return Entries(self)
@@ -420,8 +420,10 @@ class RemoteCatalogEntry(CatalogEntry):
self.http_args = (http_args or {}).copy()
if 'headers' not in self.http_args:
self.http_args['headers'] = {}
+
super(RemoteCatalogEntry, self).__init__(getenv=getenv,
getshell=getshell)
+ self._pmode = "never"
def describe(self):
return {
=====================================
intake/interface/server.py
=====================================
@@ -8,9 +8,9 @@
The simplest possible panel server. To launch a panel server containing the intake gui
run:
-panel serve intake/gui/server.py
+panel serve intake/interface/server.py
"""
-import intake
-intake.interface.servable()
+import intake.interface
+intake.interface.instance.servable()
=====================================
intake/source/derived.py
=====================================
@@ -195,7 +195,7 @@ class GenericTransform(DerivedSource):
must have a default value) - or a spec to be able to make these objects.
allow_dask: bool (optional, default True)
Whether to_dask() is expected to work, which will in turn call the
- target's to_dasK()
+ target's to_dask()
"""
def _validate_params(self):
=====================================
intake/tests/test_config.py
=====================================
@@ -12,7 +12,7 @@ import requests
import intake
from intake import config
from intake.util_tests import temp_conf, server
-
+from intake.catalog.remote import RemoteCatalog
@pytest.mark.parametrize('conf', [
{},
@@ -64,6 +64,20 @@ def test_cli():
assert r.ok
+def test_persist_modes():
+ expected_never = "never"
+ expected_default = "default"
+
+ with temp_conf({}) as fn:
+ env = os.environ.copy()
+ env["INTAKE_CONF_FILE"] = fn
+ with server(args=("-p", "5555"), env=env, wait=5555):
+ cat_never = RemoteCatalog("intake://localhost:5555", persist_mode="never")
+ assert cat_never.pmode == expected_never
+
+ cat_default = RemoteCatalog("intake://localhost:5555")
+ assert cat_default.pmode == expected_default
+
def test_conf():
with temp_conf({'port': 5555}) as fn:
env = os.environ.copy()
View it on GitLab: https://salsa.debian.org/med-team/intake/-/commit/52f4106d686bfc90bc913acfca8d7c9861e831cf
--
View it on GitLab: https://salsa.debian.org/med-team/intake/-/commit/52f4106d686bfc90bc913acfca8d7c9861e831cf
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