jaxsne 0.1.0__tar.gz

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Files changed (190) hide show
  1. jaxsne-0.1.0/.github/workflows/python-package.yml +38 -0
  2. jaxsne-0.1.0/.github/workflows/static.yml +51 -0
  3. jaxsne-0.1.0/.gitignore +5 -0
  4. jaxsne-0.1.0/.python-version +1 -0
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  30. jaxsne-0.1.0/.sl/store/git/config +19 -0
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  155. jaxsne-0.1.0/LICENSE +21 -0
  156. jaxsne-0.1.0/PKG-INFO +80 -0
  157. jaxsne-0.1.0/README.md +68 -0
  158. jaxsne-0.1.0/docs/conf.py +28 -0
  159. jaxsne-0.1.0/docs/index.rst +36 -0
  160. jaxsne-0.1.0/docs/jaxsne.rst +5 -0
  161. jaxsne-0.1.0/example.ipynb +5474 -0
  162. jaxsne-0.1.0/jaxsne/__init__.py +30 -0
  163. jaxsne-0.1.0/jaxsne/_measure.py +35 -0
  164. jaxsne-0.1.0/jaxsne/_metric.py +51 -0
  165. jaxsne-0.1.0/jaxsne/_scaling.py +72 -0
  166. jaxsne-0.1.0/jaxsne/_sne.py +174 -0
  167. jaxsne-0.1.0/jaxsne/_utils.py +31 -0
  168. jaxsne-0.1.0/jaxsne/measure.py +16 -0
  169. jaxsne-0.1.0/jaxsne/metric.py +19 -0
  170. jaxsne-0.1.0/jaxsne/py.typed +0 -0
  171. jaxsne-0.1.0/pyproject.toml +48 -0
  172. jaxsne-0.1.0/resources/psne.png +0 -0
  173. jaxsne-0.1.0/resources/ssne.gif +0 -0
  174. jaxsne-0.1.0/resources/tsne.png +0 -0
  175. jaxsne-0.1.0/tests/__init__.py +1 -0
  176. jaxsne-0.1.0/tests/test_metrics.py +66 -0
  177. jaxsne-0.1.0/tests/test_scaling.py +53 -0
  178. jaxsne-0.1.0/tests/test_sne.py +60 -0
  179. jaxsne-0.1.0/typings/jax/__init__.pyi +51 -0
  180. jaxsne-0.1.0/typings/jax/lax.pyi +9 -0
  181. jaxsne-0.1.0/typings/jax/numpy/__init__.pyi +24 -0
  182. jaxsne-0.1.0/typings/jax/numpy/linalg.pyi +4 -0
  183. jaxsne-0.1.0/typings/jax/random.pyi +5 -0
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  185. jaxsne-0.1.0/typings/jax/scipy/special.pyi +4 -0
  186. jaxsne-0.1.0/typings/numba/__init__.pyi +17 -0
  187. jaxsne-0.1.0/typings/numba/types/__init__.pyi +19 -0
  188. jaxsne-0.1.0/typings/scipy/__init__.pyi +0 -0
  189. jaxsne-0.1.0/typings/scipy/optimize/__init__.pyi +23 -0
  190. jaxsne-0.1.0/uv.lock +1816 -0
@@ -0,0 +1,38 @@
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+ # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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+ # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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+
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+ name: build
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+
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+ on:
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+ push:
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+ branches: ["main"]
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+ pull_request:
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+ branches: ["main"]
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+
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+ jobs:
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+ build:
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+ runs-on: ubuntu-latest
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+ strategy:
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+ fail-fast: false
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+ matrix:
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+ python-version: ["3.12"]
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+
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+ steps:
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+ - uses: actions/checkout@v4
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+ - name: Set up Python ${{ matrix.python-version }}
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+ uses: actions/setup-python@v3
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ python -m pip install uv
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+ uv sync
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+ - name: Check ruff format
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+ run: uv run ruff format --check
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+ - name: Check with ruff
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+ run: uv run ruff check
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+ - name: Test with pytest
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+ run: uv run pytest
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+ - name: Run mypy
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+ run: uv run mypy jaxsne
@@ -0,0 +1,51 @@
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+ # Simple workflow for deploying static content to GitHub Pages
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+ name: pages
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+
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+ on:
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+ # Runs on pushes targeting the default branch
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+ push:
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+ branches: ["main"]
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+
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+ # Allows you to run this workflow manually from the Actions tab
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+ workflow_dispatch:
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+
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+ # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
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+ permissions:
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+ contents: read
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+ pages: write
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+ id-token: write
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+
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+ # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
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+ # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
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+ concurrency:
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+ group: "pages"
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+ cancel-in-progress: false
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+
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+ jobs:
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+ # Single deploy job since we're just deploying
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+ deploy:
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+ environment:
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+ name: github-pages
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+ url: ${{ steps.deployment.outputs.page_url }}
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+ runs-on: ubuntu-latest
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+ steps:
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+ - name: Checkout
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+ uses: actions/checkout@v4
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+ - name: Setup Pages
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+ uses: actions/configure-pages@v5
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+ - name: Set up Python
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+ uses: actions/setup-python@v3
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ python -m pip install uv
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+ uv sync
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+ - name: Build site
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+ run: uv run sphinx-build -M html docs out
45
+ - name: Upload artifact
46
+ uses: actions/upload-pages-artifact@v3
47
+ with:
48
+ path: "./out/html"
49
+ - name: Deploy to GitHub Pages
50
+ id: deployment
51
+ uses: actions/deploy-pages@v4
@@ -0,0 +1,5 @@
1
+ __pycache__
2
+ out
3
+ dist
4
+ jaxsne.egg-info
5
+ .coverage
@@ -0,0 +1 @@
1
+ 3.13
File without changes
Binary file
Binary file
Binary file
@@ -0,0 +1 @@
1
+ �{ �?�|A
@@ -0,0 +1 @@
1
+ 0
@@ -0,0 +1 @@
1
+ �{ �?�|A
@@ -0,0 +1,7 @@
1
+ 2025/03/01 14:54:52 erk @(unknown) (84605) [visibility]> read 0 heads:
2
+ 2025/03/01 14:54:53 erk @(unknown) (84605) [visibility]> read 0 heads:
3
+ 2025/03/01 14:54:53 erk @(unknown) (84605) [visibility]> read 0 heads:
4
+ 2025/03/01 14:54:53 erk @(unknown) (84605) [command_finish]> clone 'https://github.com/erikbrinkman/jaxsne.git' exited 0 after 0.77 seconds
5
+ 2025/03/01 14:55:38 erk @(unknown) (85151) [command]> debugcommitmessage isl --noninteractive
6
+ 2025/03/01 14:55:38 erk @42d5d3c1f61d347e49395e60e35f6bdc88de368c (85151) [visibility]> read 0 heads:
7
+ 2025/03/01 14:55:38 erk @42d5d3c1f61d347e49395e60e35f6bdc88de368c (85151) [command_finish]> debugcommitmessage isl --noninteractive exited 0 after 0.35 seconds
@@ -0,0 +1 @@
1
+ 8uoESmoroJaxHGY2
@@ -0,0 +1,6 @@
1
+
2
+ [paths]
3
+ default = https://github.com/erikbrinkman/jaxsne.git
4
+
5
+ [remotenames]
6
+ publicheads = remote/main,remote/master
Binary file
Binary file
@@ -0,0 +1 @@
1
+ vinyl.local:84605
File without changes
@@ -0,0 +1 @@
1
+ jaxsne.git
@@ -0,0 +1,4 @@
1
+ generaldelta
2
+ revlogv1
3
+ store
4
+ treestate
@@ -0,0 +1 @@
1
+ {}
File without changes
File without changes
Binary file
Binary file
@@ -0,0 +1 @@
1
+ ���k���
@@ -0,0 +1 @@
1
+ ref: refs/heads/_unused_branch
@@ -0,0 +1,19 @@
1
+ [core]
2
+ repositoryformatversion = 0
3
+ filemode = true
4
+ bare = true
5
+ ignorecase = true
6
+ precomposeunicode = true
7
+
8
+ #### Begin maintained by Sapling ####
9
+
10
+ [maintenance "gc"]
11
+ enabled = false
12
+ [maintenance "loose-objects"]
13
+ enabled = true
14
+ [maintenance "incremental-repack"]
15
+ enabled = true
16
+ [repack]
17
+ writeBitmaps = false
18
+
19
+ #### End maintained by Sapling ####
@@ -0,0 +1 @@
1
+ Unnamed repository; edit this file 'description' to name the repository.
@@ -0,0 +1,15 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to check the commit log message taken by
4
+ # applypatch from an e-mail message.
5
+ #
6
+ # The hook should exit with non-zero status after issuing an
7
+ # appropriate message if it wants to stop the commit. The hook is
8
+ # allowed to edit the commit message file.
9
+ #
10
+ # To enable this hook, rename this file to "applypatch-msg".
11
+
12
+ . git-sh-setup
13
+ commitmsg="$(git rev-parse --git-path hooks/commit-msg)"
14
+ test -x "$commitmsg" && exec "$commitmsg" ${1+"$@"}
15
+ :
@@ -0,0 +1,24 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to check the commit log message.
4
+ # Called by "git commit" with one argument, the name of the file
5
+ # that has the commit message. The hook should exit with non-zero
6
+ # status after issuing an appropriate message if it wants to stop the
7
+ # commit. The hook is allowed to edit the commit message file.
8
+ #
9
+ # To enable this hook, rename this file to "commit-msg".
10
+
11
+ # Uncomment the below to add a Signed-off-by line to the message.
12
+ # Doing this in a hook is a bad idea in general, but the prepare-commit-msg
13
+ # hook is more suited to it.
14
+ #
15
+ # SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
16
+ # grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
17
+
18
+ # This example catches duplicate Signed-off-by lines.
19
+
20
+ test "" = "$(grep '^Signed-off-by: ' "$1" |
21
+ sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || {
22
+ echo >&2 Duplicate Signed-off-by lines.
23
+ exit 1
24
+ }
@@ -0,0 +1,174 @@
1
+ #!/usr/bin/perl
2
+
3
+ use strict;
4
+ use warnings;
5
+ use IPC::Open2;
6
+
7
+ # An example hook script to integrate Watchman
8
+ # (https://facebook.github.io/watchman/) with git to speed up detecting
9
+ # new and modified files.
10
+ #
11
+ # The hook is passed a version (currently 2) and last update token
12
+ # formatted as a string and outputs to stdout a new update token and
13
+ # all files that have been modified since the update token. Paths must
14
+ # be relative to the root of the working tree and separated by a single NUL.
15
+ #
16
+ # To enable this hook, rename this file to "query-watchman" and set
17
+ # 'git config core.fsmonitor .git/hooks/query-watchman'
18
+ #
19
+ my ($version, $last_update_token) = @ARGV;
20
+
21
+ # Uncomment for debugging
22
+ # print STDERR "$0 $version $last_update_token\n";
23
+
24
+ # Check the hook interface version
25
+ if ($version ne 2) {
26
+ die "Unsupported query-fsmonitor hook version '$version'.\n" .
27
+ "Falling back to scanning...\n";
28
+ }
29
+
30
+ my $git_work_tree = get_working_dir();
31
+
32
+ my $retry = 1;
33
+
34
+ my $json_pkg;
35
+ eval {
36
+ require JSON::XS;
37
+ $json_pkg = "JSON::XS";
38
+ 1;
39
+ } or do {
40
+ require JSON::PP;
41
+ $json_pkg = "JSON::PP";
42
+ };
43
+
44
+ launch_watchman();
45
+
46
+ sub launch_watchman {
47
+ my $o = watchman_query();
48
+ if (is_work_tree_watched($o)) {
49
+ output_result($o->{clock}, @{$o->{files}});
50
+ }
51
+ }
52
+
53
+ sub output_result {
54
+ my ($clockid, @files) = @_;
55
+
56
+ # Uncomment for debugging watchman output
57
+ # open (my $fh, ">", ".git/watchman-output.out");
58
+ # binmode $fh, ":utf8";
59
+ # print $fh "$clockid\n@files\n";
60
+ # close $fh;
61
+
62
+ binmode STDOUT, ":utf8";
63
+ print $clockid;
64
+ print "\0";
65
+ local $, = "\0";
66
+ print @files;
67
+ }
68
+
69
+ sub watchman_clock {
70
+ my $response = qx/watchman clock "$git_work_tree"/;
71
+ die "Failed to get clock id on '$git_work_tree'.\n" .
72
+ "Falling back to scanning...\n" if $? != 0;
73
+
74
+ return $json_pkg->new->utf8->decode($response);
75
+ }
76
+
77
+ sub watchman_query {
78
+ my $pid = open2(\*CHLD_OUT, \*CHLD_IN, 'watchman -j --no-pretty')
79
+ or die "open2() failed: $!\n" .
80
+ "Falling back to scanning...\n";
81
+
82
+ # In the query expression below we're asking for names of files that
83
+ # changed since $last_update_token but not from the .git folder.
84
+ #
85
+ # To accomplish this, we're using the "since" generator to use the
86
+ # recency index to select candidate nodes and "fields" to limit the
87
+ # output to file names only. Then we're using the "expression" term to
88
+ # further constrain the results.
89
+ my $last_update_line = "";
90
+ if (substr($last_update_token, 0, 1) eq "c") {
91
+ $last_update_token = "\"$last_update_token\"";
92
+ $last_update_line = qq[\n"since": $last_update_token,];
93
+ }
94
+ my $query = <<" END";
95
+ ["query", "$git_work_tree", {$last_update_line
96
+ "fields": ["name"],
97
+ "expression": ["not", ["dirname", ".git"]]
98
+ }]
99
+ END
100
+
101
+ # Uncomment for debugging the watchman query
102
+ # open (my $fh, ">", ".git/watchman-query.json");
103
+ # print $fh $query;
104
+ # close $fh;
105
+
106
+ print CHLD_IN $query;
107
+ close CHLD_IN;
108
+ my $response = do {local $/; <CHLD_OUT>};
109
+
110
+ # Uncomment for debugging the watch response
111
+ # open ($fh, ">", ".git/watchman-response.json");
112
+ # print $fh $response;
113
+ # close $fh;
114
+
115
+ die "Watchman: command returned no output.\n" .
116
+ "Falling back to scanning...\n" if $response eq "";
117
+ die "Watchman: command returned invalid output: $response\n" .
118
+ "Falling back to scanning...\n" unless $response =~ /^\{/;
119
+
120
+ return $json_pkg->new->utf8->decode($response);
121
+ }
122
+
123
+ sub is_work_tree_watched {
124
+ my ($output) = @_;
125
+ my $error = $output->{error};
126
+ if ($retry > 0 and $error and $error =~ m/unable to resolve root .* directory (.*) is not watched/) {
127
+ $retry--;
128
+ my $response = qx/watchman watch "$git_work_tree"/;
129
+ die "Failed to make watchman watch '$git_work_tree'.\n" .
130
+ "Falling back to scanning...\n" if $? != 0;
131
+ $output = $json_pkg->new->utf8->decode($response);
132
+ $error = $output->{error};
133
+ die "Watchman: $error.\n" .
134
+ "Falling back to scanning...\n" if $error;
135
+
136
+ # Uncomment for debugging watchman output
137
+ # open (my $fh, ">", ".git/watchman-output.out");
138
+ # close $fh;
139
+
140
+ # Watchman will always return all files on the first query so
141
+ # return the fast "everything is dirty" flag to git and do the
142
+ # Watchman query just to get it over with now so we won't pay
143
+ # the cost in git to look up each individual file.
144
+ my $o = watchman_clock();
145
+ $error = $output->{error};
146
+
147
+ die "Watchman: $error.\n" .
148
+ "Falling back to scanning...\n" if $error;
149
+
150
+ output_result($o->{clock}, ("/"));
151
+ $last_update_token = $o->{clock};
152
+
153
+ eval { launch_watchman() };
154
+ return 0;
155
+ }
156
+
157
+ die "Watchman: $error.\n" .
158
+ "Falling back to scanning...\n" if $error;
159
+
160
+ return 1;
161
+ }
162
+
163
+ sub get_working_dir {
164
+ my $working_dir;
165
+ if ($^O =~ 'msys' || $^O =~ 'cygwin') {
166
+ $working_dir = Win32::GetCwd();
167
+ $working_dir =~ tr/\\/\//;
168
+ } else {
169
+ require Cwd;
170
+ $working_dir = Cwd::cwd();
171
+ }
172
+
173
+ return $working_dir;
174
+ }
@@ -0,0 +1,8 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to prepare a packed repository for use over
4
+ # dumb transports.
5
+ #
6
+ # To enable this hook, rename this file to "post-update".
7
+
8
+ exec git update-server-info
@@ -0,0 +1,14 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to verify what is about to be committed
4
+ # by applypatch from an e-mail message.
5
+ #
6
+ # The hook should exit with non-zero status after issuing an
7
+ # appropriate message if it wants to stop the commit.
8
+ #
9
+ # To enable this hook, rename this file to "pre-applypatch".
10
+
11
+ . git-sh-setup
12
+ precommit="$(git rev-parse --git-path hooks/pre-commit)"
13
+ test -x "$precommit" && exec "$precommit" ${1+"$@"}
14
+ :
@@ -0,0 +1,49 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to verify what is about to be committed.
4
+ # Called by "git commit" with no arguments. The hook should
5
+ # exit with non-zero status after issuing an appropriate message if
6
+ # it wants to stop the commit.
7
+ #
8
+ # To enable this hook, rename this file to "pre-commit".
9
+
10
+ if git rev-parse --verify HEAD >/dev/null 2>&1
11
+ then
12
+ against=HEAD
13
+ else
14
+ # Initial commit: diff against an empty tree object
15
+ against=$(git hash-object -t tree /dev/null)
16
+ fi
17
+
18
+ # If you want to allow non-ASCII filenames set this variable to true.
19
+ allownonascii=$(git config --type=bool hooks.allownonascii)
20
+
21
+ # Redirect output to stderr.
22
+ exec 1>&2
23
+
24
+ # Cross platform projects tend to avoid non-ASCII filenames; prevent
25
+ # them from being added to the repository. We exploit the fact that the
26
+ # printable range starts at the space character and ends with tilde.
27
+ if [ "$allownonascii" != "true" ] &&
28
+ # Note that the use of brackets around a tr range is ok here, (it's
29
+ # even required, for portability to Solaris 10's /usr/bin/tr), since
30
+ # the square bracket bytes happen to fall in the designated range.
31
+ test $(git diff --cached --name-only --diff-filter=A -z $against |
32
+ LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
33
+ then
34
+ cat <<\EOF
35
+ Error: Attempt to add a non-ASCII file name.
36
+
37
+ This can cause problems if you want to work with people on other platforms.
38
+
39
+ To be portable it is advisable to rename the file.
40
+
41
+ If you know what you are doing you can disable this check using:
42
+
43
+ git config hooks.allownonascii true
44
+ EOF
45
+ exit 1
46
+ fi
47
+
48
+ # If there are whitespace errors, print the offending file names and fail.
49
+ exec git diff-index --check --cached $against --
@@ -0,0 +1,13 @@
1
+ #!/bin/sh
2
+ #
3
+ # An example hook script to verify what is about to be committed.
4
+ # Called by "git merge" with no arguments. The hook should
5
+ # exit with non-zero status after issuing an appropriate message to
6
+ # stderr if it wants to stop the merge commit.
7
+ #
8
+ # To enable this hook, rename this file to "pre-merge-commit".
9
+
10
+ . git-sh-setup
11
+ test -x "$GIT_DIR/hooks/pre-commit" &&
12
+ exec "$GIT_DIR/hooks/pre-commit"
13
+ :
@@ -0,0 +1,53 @@
1
+ #!/bin/sh
2
+
3
+ # An example hook script to verify what is about to be pushed. Called by "git
4
+ # push" after it has checked the remote status, but before anything has been
5
+ # pushed. If this script exits with a non-zero status nothing will be pushed.
6
+ #
7
+ # This hook is called with the following parameters:
8
+ #
9
+ # $1 -- Name of the remote to which the push is being done
10
+ # $2 -- URL to which the push is being done
11
+ #
12
+ # If pushing without using a named remote those arguments will be equal.
13
+ #
14
+ # Information about the commits which are being pushed is supplied as lines to
15
+ # the standard input in the form:
16
+ #
17
+ # <local ref> <local oid> <remote ref> <remote oid>
18
+ #
19
+ # This sample shows how to prevent push of commits where the log message starts
20
+ # with "WIP" (work in progress).
21
+
22
+ remote="$1"
23
+ url="$2"
24
+
25
+ zero=$(git hash-object --stdin </dev/null | tr '[0-9a-f]' '0')
26
+
27
+ while read local_ref local_oid remote_ref remote_oid
28
+ do
29
+ if test "$local_oid" = "$zero"
30
+ then
31
+ # Handle delete
32
+ :
33
+ else
34
+ if test "$remote_oid" = "$zero"
35
+ then
36
+ # New branch, examine all commits
37
+ range="$local_oid"
38
+ else
39
+ # Update to existing branch, examine new commits
40
+ range="$remote_oid..$local_oid"
41
+ fi
42
+
43
+ # Check for WIP commit
44
+ commit=$(git rev-list -n 1 --grep '^WIP' "$range")
45
+ if test -n "$commit"
46
+ then
47
+ echo >&2 "Found WIP commit in $local_ref, not pushing"
48
+ exit 1
49
+ fi
50
+ fi
51
+ done
52
+
53
+ exit 0