Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401

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jakirkham merged 2 commits into
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jakirkham:drop_binary_type_cast
Feb 13, 2019
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Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom
jakirkham:drop_binary_type_cast

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@jakirkhamjakirkham commented Feb 12, 2019•
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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.

xref: #372

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

@pep8speaks

pep8speaks commented Feb 12, 2019•
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Hello @jakirkham! Thanks for updating the PR.

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Comment last updated on February 13, 2019 at 06:37 Hours UTC

@jakirkhamjakirkham mentioned this pull request Feb 12, 2019
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@jhamman

jhamman commented Feb 12, 2019

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Still seems to be failing. This by the way was why I opened #393.

@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham changed the title Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham

jakirkham commented Feb 13, 2019

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That's right. Just wanted to see if that was still the case after the dust settled.

After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.

Could you please give it another look? :)

@jhamman

jhamman commented Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.

@jakirkham

jakirkham commented Feb 13, 2019

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Thanks @jhamman :)

@jakirkham
jakirkham merged commit 3c0e0f5 into zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham deleted the drop_binary_type_cast branch February 13, 2019 19:31
@jakirkhamjakirkham added this to the v2.3 milestone Feb 13, 2019
@alimanfoo

alimanfoo commented Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍

@jakirkhamjakirkham mentioned this pull request Feb 21, 2019
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@jakirkham

jakirkham commented Feb 21, 2019

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Of course. 😄

FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.

@jakirkhamjakirkham mentioned this pull request Apr 15, 2019
Merged
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@jakirkhamjakirkham mentioned this pull request Dec 3, 2020
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@jakirkham@pep8speaks@jhamman@alimanfoo
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
Merged
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Feb 12, 2019•

edited

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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
pep8speaks
commented
Feb 12, 2019•

edited

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Hello @jakirkham! Thanks for updating the PR.
Line 4:80: E501 line too long (80 > 79 characters)
Line 8:80: E501 line too long (86 > 79 characters)
Line 9:80: E501 line too long (82 > 79 characters)
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Line 1861:80: E501 line too long (86 > 79 characters)
Line 1898:80: E501 line too long (80 > 79 characters)
Line 2110:80: E501 line too long (80 > 79 characters)
Line 2215:80: E501 line too long (80 > 79 characters)
Line 2278:80: E501 line too long (80 > 79 characters)
Line 2292:80: E501 line too long (86 > 79 characters)
Line 2325:80: E501 line too long (85 > 79 characters)
Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
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7 tasks
@jhamman
jhamman
commented
Feb 12, 2019

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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
jakirkham
commented
Feb 13, 2019

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That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
jhamman
commented
Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
jakirkham
commented
Feb 13, 2019

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Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
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Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
mentioned this pull request
Feb 21, 2019
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@jakirkham
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Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

7 tasks
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
 Merged

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@jakirkham@pep8speaks@jhamman@alimanfoo

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
Merged
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
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@jakirkham
@jakirkhamjakirkham
commented
Feb 12, 2019•

edited

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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
pep8speaks
commented
Feb 12, 2019•

edited

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Hello @jakirkham! Thanks for updating the PR.
Line 4:80: E501 line too long (80 > 79 characters)
Line 8:80: E501 line too long (86 > 79 characters)
Line 9:80: E501 line too long (82 > 79 characters)
Line 10:80: E501 line too long (84 > 79 characters)
Line 11:80: E501 line too long (84 > 79 characters)
Line 12:80: E501 line too long (85 > 79 characters)
Line 13:80: E501 line too long (81 > 79 characters)
Line 14:80: E501 line too long (89 > 79 characters)
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Line 922:80: E501 line too long (80 > 79 characters)
Line 937:80: E501 line too long (80 > 79 characters)
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Line 1025:80: E501 line too long (83 > 79 characters)
Line 1072:80: E501 line too long (80 > 79 characters)
Line 1074:80: E501 line too long (83 > 79 characters)
Line 1085:80: E501 line too long (80 > 79 characters)
Line 1097:80: E501 line too long (80 > 79 characters)
Line 1104:80: E501 line too long (88 > 79 characters)
Line 1108:80: E501 line too long (82 > 79 characters)
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Line 1159:80: E501 line too long (89 > 79 characters)
Line 1333:80: E501 line too long (85 > 79 characters)
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Line 1346:80: E501 line too long (80 > 79 characters)
Line 1359:80: E501 line too long (80 > 79 characters)
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Line 1592:80: E501 line too long (84 > 79 characters)
Line 1593:80: E501 line too long (89 > 79 characters)
Line 1597:80: E501 line too long (84 > 79 characters)
Line 1598:80: E501 line too long (87 > 79 characters)
Line 1701:80: E501 line too long (81 > 79 characters)
Line 1702:80: E501 line too long (80 > 79 characters)
Line 1711:80: E501 line too long (87 > 79 characters)
Line 1720:80: E501 line too long (90 > 79 characters)
Line 1727:80: E501 line too long (91 > 79 characters)
Line 1731:80: E501 line too long (91 > 79 characters)
Line 1749:80: E501 line too long (82 > 79 characters)
Line 1750:80: E501 line too long (89 > 79 characters)
Line 1755:80: E501 line too long (82 > 79 characters)
Line 1797:80: E501 line too long (83 > 79 characters)
Line 1813:80: E501 line too long (86 > 79 characters)
Line 1861:80: E501 line too long (86 > 79 characters)
Line 1898:80: E501 line too long (80 > 79 characters)
Line 2110:80: E501 line too long (80 > 79 characters)
Line 2215:80: E501 line too long (80 > 79 characters)
Line 2278:80: E501 line too long (80 > 79 characters)
Line 2292:80: E501 line too long (86 > 79 characters)
Line 2325:80: E501 line too long (85 > 79 characters)
Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
 Merged

7 tasks
@jhamman
jhamman
commented
Feb 12, 2019

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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
jakirkham
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Feb 13, 2019

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That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
jhamman
commented
Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
jakirkham
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Feb 13, 2019

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Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
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Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
mentioned this pull request
Feb 21, 2019
 Closed

8 tasks
@jakirkham
jakirkham
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Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

7 tasks
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
 Merged

6 tasks
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@jakirkham@pep8speaks@jhamman@alimanfoo

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
Merged
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Feb 12, 2019•

edited

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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
pep8speaks
commented
Feb 12, 2019•

edited

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Hello @jakirkham! Thanks for updating the PR.
Line 4:80: E501 line too long (80 > 79 characters)
Line 8:80: E501 line too long (86 > 79 characters)
Line 9:80: E501 line too long (82 > 79 characters)
Line 10:80: E501 line too long (84 > 79 characters)
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Line 102:80: E501 line too long (83 > 79 characters)
Line 125:80: E501 line too long (84 > 79 characters)
Line 151:80: E501 line too long (85 > 79 characters)
Line 152:80: E501 line too long (83 > 79 characters)
Line 164:80: E501 line too long (85 > 79 characters)
Line 210:80: E501 line too long (92 > 79 characters)
Line 281:80: E501 line too long (86 > 79 characters)
Line 308:80: E501 line too long (80 > 79 characters)
Line 317:80: E501 line too long (90 > 79 characters)
Line 326:80: E501 line too long (85 > 79 characters)
Line 327:80: E501 line too long (80 > 79 characters)
Line 377:80: E501 line too long (81 > 79 characters)
Line 380:80: E501 line too long (83 > 79 characters)
Line 382:80: E501 line too long (89 > 79 characters)
Line 406:80: E501 line too long (94 > 79 characters)
Line 467:80: E501 line too long (80 > 79 characters)
Line 673:80: E501 line too long (80 > 79 characters)
Line 705:80: E501 line too long (84 > 79 characters)
Line 706:80: E501 line too long (83 > 79 characters)
Line 754:80: E501 line too long (83 > 79 characters)
Line 765:80: E501 line too long (87 > 79 characters)
Line 922:80: E501 line too long (80 > 79 characters)
Line 937:80: E501 line too long (80 > 79 characters)
Line 1014:80: E501 line too long (85 > 79 characters)
Line 1024:80: E501 line too long (82 > 79 characters)
Line 1025:80: E501 line too long (83 > 79 characters)
Line 1072:80: E501 line too long (80 > 79 characters)
Line 1074:80: E501 line too long (83 > 79 characters)
Line 1085:80: E501 line too long (80 > 79 characters)
Line 1097:80: E501 line too long (80 > 79 characters)
Line 1104:80: E501 line too long (88 > 79 characters)
Line 1108:80: E501 line too long (82 > 79 characters)
Line 1117:80: E501 line too long (88 > 79 characters)
Line 1126:80: E501 line too long (84 > 79 characters)
Line 1127:80: E501 line too long (83 > 79 characters)
Line 1141:80: E501 line too long (87 > 79 characters)
Line 1145:80: E501 line too long (80 > 79 characters)
Line 1159:80: E501 line too long (89 > 79 characters)
Line 1333:80: E501 line too long (85 > 79 characters)
Line 1336:80: E501 line too long (88 > 79 characters)
Line 1346:80: E501 line too long (80 > 79 characters)
Line 1359:80: E501 line too long (80 > 79 characters)
Line 1361:80: E501 line too long (80 > 79 characters)
Line 1365:80: E501 line too long (84 > 79 characters)
Line 1376:80: E501 line too long (80 > 79 characters)
Line 1388:80: E501 line too long (80 > 79 characters)
Line 1390:80: E501 line too long (80 > 79 characters)
Line 1394:80: E501 line too long (82 > 79 characters)
Line 1395:80: E501 line too long (83 > 79 characters)
Line 1418:80: E501 line too long (83 > 79 characters)
Line 1457:80: E501 line too long (83 > 79 characters)
Line 1460:80: E501 line too long (87 > 79 characters)
Line 1527:80: E501 line too long (83 > 79 characters)
Line 1536:80: E501 line too long (87 > 79 characters)
Line 1547:80: E501 line too long (80 > 79 characters)
Line 1560:80: E501 line too long (80 > 79 characters)
Line 1562:80: E501 line too long (80 > 79 characters)
Line 1566:80: E501 line too long (84 > 79 characters)
Line 1572:80: E501 line too long (86 > 79 characters)
Line 1573:80: E501 line too long (90 > 79 characters)
Line 1575:80: E501 line too long (87 > 79 characters)
Line 1576:80: E501 line too long (86 > 79 characters)
Line 1583:80: E501 line too long (89 > 79 characters)
Line 1584:80: E501 line too long (87 > 79 characters)
Line 1591:80: E501 line too long (83 > 79 characters)
Line 1592:80: E501 line too long (84 > 79 characters)
Line 1593:80: E501 line too long (89 > 79 characters)
Line 1597:80: E501 line too long (84 > 79 characters)
Line 1598:80: E501 line too long (87 > 79 characters)
Line 1701:80: E501 line too long (81 > 79 characters)
Line 1702:80: E501 line too long (80 > 79 characters)
Line 1711:80: E501 line too long (87 > 79 characters)
Line 1720:80: E501 line too long (90 > 79 characters)
Line 1727:80: E501 line too long (91 > 79 characters)
Line 1731:80: E501 line too long (91 > 79 characters)
Line 1749:80: E501 line too long (82 > 79 characters)
Line 1750:80: E501 line too long (89 > 79 characters)
Line 1755:80: E501 line too long (82 > 79 characters)
Line 1797:80: E501 line too long (83 > 79 characters)
Line 1813:80: E501 line too long (86 > 79 characters)
Line 1861:80: E501 line too long (86 > 79 characters)
Line 1898:80: E501 line too long (80 > 79 characters)
Line 2110:80: E501 line too long (80 > 79 characters)
Line 2215:80: E501 line too long (80 > 79 characters)
Line 2278:80: E501 line too long (80 > 79 characters)
Line 2292:80: E501 line too long (86 > 79 characters)
Line 2325:80: E501 line too long (85 > 79 characters)
Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
 Merged

7 tasks
@jhamman
jhamman
commented
Feb 12, 2019

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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
jakirkham
commented
Feb 13, 2019

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MemberAuthor
That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
jhamman
commented
Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
jakirkham
commented
Feb 13, 2019

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MemberAuthor
Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
alimanfoo
commented
Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
mentioned this pull request
Feb 21, 2019
 Closed

8 tasks
@jakirkham
jakirkham
commented
Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

7 tasks
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
 Merged

6 tasks
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Milestone

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4 participants

@jakirkham@pep8speaks@jhamman@alimanfoo

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
Merged
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Feb 12, 2019•

edited

Loading

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Member
Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
pep8speaks
commented
Feb 12, 2019•

edited

Loading

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Hello @jakirkham! Thanks for updating the PR.
Line 4:80: E501 line too long (80 > 79 characters)
Line 8:80: E501 line too long (86 > 79 characters)
Line 9:80: E501 line too long (82 > 79 characters)
Line 10:80: E501 line too long (84 > 79 characters)
Line 11:80: E501 line too long (84 > 79 characters)
Line 12:80: E501 line too long (85 > 79 characters)
Line 13:80: E501 line too long (81 > 79 characters)
Line 14:80: E501 line too long (89 > 79 characters)
Line 43:80: E501 line too long (84 > 79 characters)
Line 44:80: E501 line too long (80 > 79 characters)
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Line 2325:80: E501 line too long (85 > 79 characters)
Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
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7 tasks
@jhamman
jhamman
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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
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That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
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Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
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Feb 13, 2019

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Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
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Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
mentioned this pull request
Feb 21, 2019
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@jakirkham
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Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

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@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
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@jakirkham@pep8speaks@jhamman@alimanfoo

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
Merged
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
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@jakirkham
@jakirkhamjakirkham
commented
Feb 12, 2019•

edited

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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
pep8speaks
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Feb 12, 2019•

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Hello @jakirkham! Thanks for updating the PR.
Line 4:80: E501 line too long (80 > 79 characters)
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Line 1598:80: E501 line too long (87 > 79 characters)
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Line 1702:80: E501 line too long (80 > 79 characters)
Line 1711:80: E501 line too long (87 > 79 characters)
Line 1720:80: E501 line too long (90 > 79 characters)
Line 1727:80: E501 line too long (91 > 79 characters)
Line 1731:80: E501 line too long (91 > 79 characters)
Line 1749:80: E501 line too long (82 > 79 characters)
Line 1750:80: E501 line too long (89 > 79 characters)
Line 1755:80: E501 line too long (82 > 79 characters)
Line 1797:80: E501 line too long (83 > 79 characters)
Line 1813:80: E501 line too long (86 > 79 characters)
Line 1861:80: E501 line too long (86 > 79 characters)
Line 1898:80: E501 line too long (80 > 79 characters)
Line 2110:80: E501 line too long (80 > 79 characters)
Line 2215:80: E501 line too long (80 > 79 characters)
Line 2278:80: E501 line too long (80 > 79 characters)
Line 2292:80: E501 line too long (86 > 79 characters)
Line 2325:80: E501 line too long (85 > 79 characters)
Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
 Merged

7 tasks
@jhamman
jhamman
commented
Feb 12, 2019

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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
jakirkham
commented
Feb 13, 2019

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That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
jhamman
commented
Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
jakirkham
commented
Feb 13, 2019

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Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
alimanfoo
commented
Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
mentioned this pull request
Feb 21, 2019
 Closed

8 tasks
@jakirkham
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commented
Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

7 tasks
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
 Merged

6 tasks
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@jakirkham@pep8speaks@jhamman@alimanfoo

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
Merged
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
zarr-developers:masterfrom 
jakirkham:drop_binary_type_cast
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Feb 12, 2019•

edited

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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
pep8speaks
commented
Feb 12, 2019•

edited

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Hello @jakirkham! Thanks for updating the PR.
Line 4:80: E501 line too long (80 > 79 characters)
Line 8:80: E501 line too long (86 > 79 characters)
Line 9:80: E501 line too long (82 > 79 characters)
Line 10:80: E501 line too long (84 > 79 characters)
Line 11:80: E501 line too long (84 > 79 characters)
Line 12:80: E501 line too long (85 > 79 characters)
Line 13:80: E501 line too long (81 > 79 characters)
Line 14:80: E501 line too long (89 > 79 characters)
Line 43:80: E501 line too long (84 > 79 characters)
Line 44:80: E501 line too long (80 > 79 characters)
Line 102:80: E501 line too long (83 > 79 characters)
Line 125:80: E501 line too long (84 > 79 characters)
Line 151:80: E501 line too long (85 > 79 characters)
Line 152:80: E501 line too long (83 > 79 characters)
Line 164:80: E501 line too long (85 > 79 characters)
Line 210:80: E501 line too long (92 > 79 characters)
Line 281:80: E501 line too long (86 > 79 characters)
Line 308:80: E501 line too long (80 > 79 characters)
Line 317:80: E501 line too long (90 > 79 characters)
Line 326:80: E501 line too long (85 > 79 characters)
Line 327:80: E501 line too long (80 > 79 characters)
Line 377:80: E501 line too long (81 > 79 characters)
Line 380:80: E501 line too long (83 > 79 characters)
Line 382:80: E501 line too long (89 > 79 characters)
Line 406:80: E501 line too long (94 > 79 characters)
Line 467:80: E501 line too long (80 > 79 characters)
Line 673:80: E501 line too long (80 > 79 characters)
Line 705:80: E501 line too long (84 > 79 characters)
Line 706:80: E501 line too long (83 > 79 characters)
Line 754:80: E501 line too long (83 > 79 characters)
Line 765:80: E501 line too long (87 > 79 characters)
Line 922:80: E501 line too long (80 > 79 characters)
Line 937:80: E501 line too long (80 > 79 characters)
Line 1014:80: E501 line too long (85 > 79 characters)
Line 1024:80: E501 line too long (82 > 79 characters)
Line 1025:80: E501 line too long (83 > 79 characters)
Line 1072:80: E501 line too long (80 > 79 characters)
Line 1074:80: E501 line too long (83 > 79 characters)
Line 1085:80: E501 line too long (80 > 79 characters)
Line 1097:80: E501 line too long (80 > 79 characters)
Line 1104:80: E501 line too long (88 > 79 characters)
Line 1108:80: E501 line too long (82 > 79 characters)
Line 1117:80: E501 line too long (88 > 79 characters)
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Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
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@jhamman
jhamman
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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
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That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
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Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
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Feb 13, 2019

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Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
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Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
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Feb 21, 2019
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@jakirkham
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Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

7 tasks
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
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, 'i');
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} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Use binary_type in MongoDBStore.__getitem__ for Python 2 only - #401
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jakirkham merged 2 commits into
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jakirkham:drop_binary_type_cast
Feb 13, 2019
Merged
Use binary_type in MongoDBStore.__getitem__ for Python 2 only#401
jakirkham merged 2 commits into
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jakirkham:drop_binary_type_cast
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@jakirkham
@jakirkhamjakirkham
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Feb 12, 2019•

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Previously there were some test failures on Python 2 and referenced in this comment (and later discussion). Turns out on Python 2 a bson.Binary instance is returned, which subclasses bytes, as explained in the docs. So the coercion to bytes is only needed on Python 2 to convert bson.Binary to bytes. As Python 3 already returns a bytes instance, there is nothing we need to do there. Thus we restrict the binary_type call to Python 2. Should avoid a copy on Python 3.
xref: #372
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  Docs build locally (e.g., run tox -e docs)
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@pep8speaks
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Hello @jakirkham! Thanks for updating the PR.
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Comment last updated on February 13, 2019 at 06:37 Hours UTC
@jakirkhamjakirkham
mentioned this pull request
Feb 12, 2019
 Merged

7 tasks
@jhamman
jhamman
commented
Feb 12, 2019

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Still seems to be failing. This by the way was why I opened #393.
@jakirkham
Coerce PyMongo values to binary_type on Python 2
efa3ee9
On both Python 2 and Python 3, PyMongo converts `binary_type` (i.e.
`bytes`) to BSON type 5 (Binary data) with subtype 0 to store in the
MongoDB instance. When reading that data back out, PyMongo handles BSON
type 5 (Binary data) with subtype 0 differently depending on the Python
version.
On Python 2, it creates a `bson.Binary` instance with the data. Normally
we would coerce this to a `bytes` object using `ensure_bytes`. However
that fails as `bson.Binary` is a subclass of `bytes`. So instead we
explicitly force it to `bytes` (i.e. `binary_type`). On Python 3,
PyMongo automatically converts the data to `bytes`. Thus we don't need
to do anything there.
ref: http://api.mongodb.com/python/current/python3.html#id3
ref: http://api.mongodb.com/python/current/api/bson/binary.html#bson.binary.Binary
@jakirkhamjakirkham
changed the title
Drop binary_type cast in MongoDBStore.__getitem__Use binary_type in MongoDBStore.__getitem__ for Python 2 onlyFeb 13, 2019
@jakirkham
jakirkham
commented
Feb 13, 2019

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That's right. Just wanted to see if that was still the case after the dust settled.
After doing a little research, it looks like we can safely constrain this coercion to Python 2 only. Have updated the PR to do that. Should make it easier for us to remember to remove when we do drop Python 2.
Could you please give it another look? :)
@jhamman
jhamman
commented
Feb 13, 2019

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yep, this looks right. I agree, this will make it easier to undo when PY2 goes away. Thanks.
@jakirkham
jakirkham
commented
Feb 13, 2019

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Thanks @jhamman :)
@jakirkham
jakirkham
merged commit 3c0e0f5
into
zarr-developers:masterFeb 13, 2019
@jakirkham
jakirkham
deleted the

drop_binary_type_cast

branch
February 13, 2019 19:31
@jakirkhamjakirkham
added this to the v2.3 milestone
Feb 13, 2019
@alimanfoo
alimanfoo
commented
Feb 19, 2019

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Thanks @jakirkham for this, nice to know exactly what's going on 👍
@jakirkhamjakirkham
mentioned this pull request
Feb 21, 2019
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@jakirkham
jakirkham
commented
Feb 21, 2019

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Of course. 😄
FWIW I think we can get a better handle on this behavior by adding a flag to the ensure_* functions to handle subclasses of the expected type (e.g. bytes in this case). Opened PR ( zarr-developers/numcodecs#173 ) along these lines.
@jakirkhamjakirkham
mentioned this pull request
Apr 15, 2019
 Merged

7 tasks
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020
 Merged

6 tasks
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