vizibridge 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- vizibridge-0.1.0/.gitignore +74 -0
- vizibridge-0.1.0/.gitlab-ci.yml +54 -0
- vizibridge-0.1.0/Cargo.lock +310 -0
- vizibridge-0.1.0/Cargo.toml +14 -0
- vizibridge-0.1.0/Dockerfile +4 -0
- vizibridge-0.1.0/LICENSE +21 -0
- vizibridge-0.1.0/PKG-INFO +11 -0
- vizibridge-0.1.0/pyproject.toml +24 -0
- vizibridge-0.1.0/python/vizibridge/__init__.py +43 -0
- vizibridge-0.1.0/rust-toolchain.toml +2 -0
- vizibridge-0.1.0/src/lib.rs +107 -0
|
@@ -0,0 +1,74 @@
|
|
|
1
|
+
/target
|
|
2
|
+
|
|
3
|
+
Cargo.lock
|
|
4
|
+
.github
|
|
5
|
+
# Byte-compiled / optimized / DLL files
|
|
6
|
+
__pycache__/
|
|
7
|
+
.pytest_cache/
|
|
8
|
+
*.py[cod]
|
|
9
|
+
|
|
10
|
+
# C extensions
|
|
11
|
+
*.so
|
|
12
|
+
|
|
13
|
+
# Distribution / packaging
|
|
14
|
+
.Python
|
|
15
|
+
.venv/
|
|
16
|
+
env/
|
|
17
|
+
bin/
|
|
18
|
+
build/
|
|
19
|
+
develop-eggs/
|
|
20
|
+
dist/
|
|
21
|
+
eggs/
|
|
22
|
+
lib/
|
|
23
|
+
lib64/
|
|
24
|
+
parts/
|
|
25
|
+
sdist/
|
|
26
|
+
var/
|
|
27
|
+
include/
|
|
28
|
+
man/
|
|
29
|
+
venv/
|
|
30
|
+
*.egg-info/
|
|
31
|
+
.installed.cfg
|
|
32
|
+
*.egg
|
|
33
|
+
|
|
34
|
+
# Installer logs
|
|
35
|
+
pip-log.txt
|
|
36
|
+
pip-delete-this-directory.txt
|
|
37
|
+
pip-selfcheck.json
|
|
38
|
+
|
|
39
|
+
# Unit test / coverage reports
|
|
40
|
+
htmlcov/
|
|
41
|
+
.tox/
|
|
42
|
+
.coverage
|
|
43
|
+
.cache
|
|
44
|
+
nosetests.xml
|
|
45
|
+
coverage.xml
|
|
46
|
+
|
|
47
|
+
# Translations
|
|
48
|
+
*.mo
|
|
49
|
+
|
|
50
|
+
# Mr Developer
|
|
51
|
+
.mr.developer.cfg
|
|
52
|
+
.project
|
|
53
|
+
.pydevproject
|
|
54
|
+
|
|
55
|
+
# Rope
|
|
56
|
+
.ropeproject
|
|
57
|
+
|
|
58
|
+
# Django stuff:
|
|
59
|
+
*.log
|
|
60
|
+
*.pot
|
|
61
|
+
|
|
62
|
+
.DS_Store
|
|
63
|
+
|
|
64
|
+
# Sphinx documentation
|
|
65
|
+
docs/_build/
|
|
66
|
+
|
|
67
|
+
# PyCharm
|
|
68
|
+
.idea/
|
|
69
|
+
|
|
70
|
+
# VSCode
|
|
71
|
+
.vscode/
|
|
72
|
+
|
|
73
|
+
# Pyenv
|
|
74
|
+
.python-version
|
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
stages: # List of stages for jobs, and their order of execution
|
|
2
|
+
- build
|
|
3
|
+
- compile
|
|
4
|
+
- release
|
|
5
|
+
|
|
6
|
+
build-job: # This job runs in the build stage, which runs first.
|
|
7
|
+
stage: build
|
|
8
|
+
tags:
|
|
9
|
+
- ci.inria.fr
|
|
10
|
+
- medium
|
|
11
|
+
image: docker:stable
|
|
12
|
+
script:
|
|
13
|
+
- docker build -t "$CI_REGISTRY_IMAGE/vizibridge_cont" .
|
|
14
|
+
- docker login -u gitlab-ci-token -p "$CI_JOB_TOKEN" "$CI_REGISTRY"
|
|
15
|
+
- docker push "$CI_REGISTRY_IMAGE/vizibridge_cont"
|
|
16
|
+
|
|
17
|
+
compile:
|
|
18
|
+
stage: compile
|
|
19
|
+
tags:
|
|
20
|
+
- ci.inria.fr
|
|
21
|
+
- medium
|
|
22
|
+
image: "$CI_REGISTRY_IMAGE/vizibridge_cont"
|
|
23
|
+
script:
|
|
24
|
+
- echo C_JOB_ID=$CI_JOB_ID >> generate_executables.env
|
|
25
|
+
- maturin build --release
|
|
26
|
+
- file_path=$(ls target/wheels/*)
|
|
27
|
+
- echo F_L_x86_64=$(basename $file_path) >> generate_executables.env
|
|
28
|
+
- cat generate_executables.env
|
|
29
|
+
|
|
30
|
+
artifacts:
|
|
31
|
+
paths:
|
|
32
|
+
- ./target/wheels/*
|
|
33
|
+
reports:
|
|
34
|
+
dotenv: generate_executables.env
|
|
35
|
+
|
|
36
|
+
release_job:
|
|
37
|
+
stage: release
|
|
38
|
+
tags:
|
|
39
|
+
- ci.inria.fr
|
|
40
|
+
- medium
|
|
41
|
+
image: registry.gitlab.com/gitlab-org/release-cli:latest
|
|
42
|
+
rules:
|
|
43
|
+
- if: $CI_COMMIT_TAG # Run this job when a tag is created
|
|
44
|
+
script:
|
|
45
|
+
- echo "running release_job"
|
|
46
|
+
- echo "Compile job_id $C_JOB_ID"
|
|
47
|
+
- echo "url https://gitlab.inria.fr/cpaperma/vizibridge/-/jobs/${C_JOB_ID}/artifacts/raw/target/wheels/${F_L_x86_64}"
|
|
48
|
+
release: # See https://docs.gitlab.com/ee/ci/yaml/#release for available properties
|
|
49
|
+
tag_name: '$CI_COMMIT_TAG'
|
|
50
|
+
description: '$CI_COMMIT_TAG'
|
|
51
|
+
assets:
|
|
52
|
+
links:
|
|
53
|
+
- name: "Linux/X86_64"
|
|
54
|
+
url: "https://gitlab.inria.fr/cpaperma/vizibridge/-/jobs/${C_JOB_ID}/artifacts/raw/target/wheels/${F_L_x86_64}"
|
|
@@ -0,0 +1,310 @@
|
|
|
1
|
+
# This file is automatically @generated by Cargo.
|
|
2
|
+
# It is not intended for manual editing.
|
|
3
|
+
version = 3
|
|
4
|
+
|
|
5
|
+
[[package]]
|
|
6
|
+
name = "autocfg"
|
|
7
|
+
version = "1.2.0"
|
|
8
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
9
|
+
checksum = "f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80"
|
|
10
|
+
|
|
11
|
+
[[package]]
|
|
12
|
+
name = "bitflags"
|
|
13
|
+
version = "1.3.2"
|
|
14
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
15
|
+
checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
|
|
16
|
+
|
|
17
|
+
[[package]]
|
|
18
|
+
name = "cfg-if"
|
|
19
|
+
version = "1.0.0"
|
|
20
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
21
|
+
checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
|
|
22
|
+
|
|
23
|
+
[[package]]
|
|
24
|
+
name = "heck"
|
|
25
|
+
version = "0.4.1"
|
|
26
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
27
|
+
checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
|
|
28
|
+
|
|
29
|
+
[[package]]
|
|
30
|
+
name = "indoc"
|
|
31
|
+
version = "2.0.5"
|
|
32
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
33
|
+
checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5"
|
|
34
|
+
|
|
35
|
+
[[package]]
|
|
36
|
+
name = "libc"
|
|
37
|
+
version = "0.2.153"
|
|
38
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
39
|
+
checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
|
|
40
|
+
|
|
41
|
+
[[package]]
|
|
42
|
+
name = "lock_api"
|
|
43
|
+
version = "0.4.11"
|
|
44
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
45
|
+
checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
|
|
46
|
+
dependencies = [
|
|
47
|
+
"autocfg",
|
|
48
|
+
"scopeguard",
|
|
49
|
+
]
|
|
50
|
+
|
|
51
|
+
[[package]]
|
|
52
|
+
name = "log"
|
|
53
|
+
version = "0.4.21"
|
|
54
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
55
|
+
checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
|
|
56
|
+
|
|
57
|
+
[[package]]
|
|
58
|
+
name = "memoffset"
|
|
59
|
+
version = "0.9.1"
|
|
60
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
61
|
+
checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
|
|
62
|
+
dependencies = [
|
|
63
|
+
"autocfg",
|
|
64
|
+
]
|
|
65
|
+
|
|
66
|
+
[[package]]
|
|
67
|
+
name = "once_cell"
|
|
68
|
+
version = "1.19.0"
|
|
69
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
70
|
+
checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
|
|
71
|
+
|
|
72
|
+
[[package]]
|
|
73
|
+
name = "parking_lot"
|
|
74
|
+
version = "0.12.1"
|
|
75
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
76
|
+
checksum = "3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f"
|
|
77
|
+
dependencies = [
|
|
78
|
+
"lock_api",
|
|
79
|
+
"parking_lot_core",
|
|
80
|
+
]
|
|
81
|
+
|
|
82
|
+
[[package]]
|
|
83
|
+
name = "parking_lot_core"
|
|
84
|
+
version = "0.9.9"
|
|
85
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
86
|
+
checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
|
|
87
|
+
dependencies = [
|
|
88
|
+
"cfg-if",
|
|
89
|
+
"libc",
|
|
90
|
+
"redox_syscall",
|
|
91
|
+
"smallvec",
|
|
92
|
+
"windows-targets",
|
|
93
|
+
]
|
|
94
|
+
|
|
95
|
+
[[package]]
|
|
96
|
+
name = "portable-atomic"
|
|
97
|
+
version = "1.6.0"
|
|
98
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
99
|
+
checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
|
|
100
|
+
|
|
101
|
+
[[package]]
|
|
102
|
+
name = "proc-macro2"
|
|
103
|
+
version = "1.0.79"
|
|
104
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
105
|
+
checksum = "e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e"
|
|
106
|
+
dependencies = [
|
|
107
|
+
"unicode-ident",
|
|
108
|
+
]
|
|
109
|
+
|
|
110
|
+
[[package]]
|
|
111
|
+
name = "pyo3"
|
|
112
|
+
version = "0.20.3"
|
|
113
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
114
|
+
checksum = "53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233"
|
|
115
|
+
dependencies = [
|
|
116
|
+
"cfg-if",
|
|
117
|
+
"indoc",
|
|
118
|
+
"libc",
|
|
119
|
+
"memoffset",
|
|
120
|
+
"parking_lot",
|
|
121
|
+
"portable-atomic",
|
|
122
|
+
"pyo3-build-config",
|
|
123
|
+
"pyo3-ffi",
|
|
124
|
+
"pyo3-macros",
|
|
125
|
+
"unindent",
|
|
126
|
+
]
|
|
127
|
+
|
|
128
|
+
[[package]]
|
|
129
|
+
name = "pyo3-build-config"
|
|
130
|
+
version = "0.20.3"
|
|
131
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
132
|
+
checksum = "deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7"
|
|
133
|
+
dependencies = [
|
|
134
|
+
"once_cell",
|
|
135
|
+
"target-lexicon",
|
|
136
|
+
]
|
|
137
|
+
|
|
138
|
+
[[package]]
|
|
139
|
+
name = "pyo3-ffi"
|
|
140
|
+
version = "0.20.3"
|
|
141
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
142
|
+
checksum = "62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa"
|
|
143
|
+
dependencies = [
|
|
144
|
+
"libc",
|
|
145
|
+
"pyo3-build-config",
|
|
146
|
+
]
|
|
147
|
+
|
|
148
|
+
[[package]]
|
|
149
|
+
name = "pyo3-macros"
|
|
150
|
+
version = "0.20.3"
|
|
151
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
152
|
+
checksum = "7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158"
|
|
153
|
+
dependencies = [
|
|
154
|
+
"proc-macro2",
|
|
155
|
+
"pyo3-macros-backend",
|
|
156
|
+
"quote",
|
|
157
|
+
"syn",
|
|
158
|
+
]
|
|
159
|
+
|
|
160
|
+
[[package]]
|
|
161
|
+
name = "pyo3-macros-backend"
|
|
162
|
+
version = "0.20.3"
|
|
163
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
164
|
+
checksum = "7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185"
|
|
165
|
+
dependencies = [
|
|
166
|
+
"heck",
|
|
167
|
+
"proc-macro2",
|
|
168
|
+
"pyo3-build-config",
|
|
169
|
+
"quote",
|
|
170
|
+
"syn",
|
|
171
|
+
]
|
|
172
|
+
|
|
173
|
+
[[package]]
|
|
174
|
+
name = "quote"
|
|
175
|
+
version = "1.0.36"
|
|
176
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
177
|
+
checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
|
|
178
|
+
dependencies = [
|
|
179
|
+
"proc-macro2",
|
|
180
|
+
]
|
|
181
|
+
|
|
182
|
+
[[package]]
|
|
183
|
+
name = "redox_syscall"
|
|
184
|
+
version = "0.4.1"
|
|
185
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
186
|
+
checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
|
|
187
|
+
dependencies = [
|
|
188
|
+
"bitflags",
|
|
189
|
+
]
|
|
190
|
+
|
|
191
|
+
[[package]]
|
|
192
|
+
name = "scopeguard"
|
|
193
|
+
version = "1.2.0"
|
|
194
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
195
|
+
checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
|
|
196
|
+
|
|
197
|
+
[[package]]
|
|
198
|
+
name = "seq-macro"
|
|
199
|
+
version = "0.3.5"
|
|
200
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
201
|
+
checksum = "a3f0bf26fd526d2a95683cd0f87bf103b8539e2ca1ef48ce002d67aad59aa0b4"
|
|
202
|
+
|
|
203
|
+
[[package]]
|
|
204
|
+
name = "smallvec"
|
|
205
|
+
version = "1.13.2"
|
|
206
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
207
|
+
checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
|
|
208
|
+
|
|
209
|
+
[[package]]
|
|
210
|
+
name = "syn"
|
|
211
|
+
version = "2.0.58"
|
|
212
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
213
|
+
checksum = "44cfb93f38070beee36b3fef7d4f5a16f27751d94b187b666a5cc5e9b0d30687"
|
|
214
|
+
dependencies = [
|
|
215
|
+
"proc-macro2",
|
|
216
|
+
"quote",
|
|
217
|
+
"unicode-ident",
|
|
218
|
+
]
|
|
219
|
+
|
|
220
|
+
[[package]]
|
|
221
|
+
name = "target-lexicon"
|
|
222
|
+
version = "0.12.14"
|
|
223
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
224
|
+
checksum = "e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f"
|
|
225
|
+
|
|
226
|
+
[[package]]
|
|
227
|
+
name = "unicode-ident"
|
|
228
|
+
version = "1.0.12"
|
|
229
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
230
|
+
checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
|
|
231
|
+
|
|
232
|
+
[[package]]
|
|
233
|
+
name = "unindent"
|
|
234
|
+
version = "0.2.3"
|
|
235
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
236
|
+
checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
|
|
237
|
+
|
|
238
|
+
[[package]]
|
|
239
|
+
name = "vizibridge"
|
|
240
|
+
version = "0.1.0"
|
|
241
|
+
dependencies = [
|
|
242
|
+
"pyo3",
|
|
243
|
+
"seq-macro",
|
|
244
|
+
"vizitig-lib",
|
|
245
|
+
]
|
|
246
|
+
|
|
247
|
+
[[package]]
|
|
248
|
+
name = "vizitig-lib"
|
|
249
|
+
version = "0.1.0"
|
|
250
|
+
source = "git+https://gitlab.inria.fr/cpaperma/vizicomp.git#cd737b028d8f2bd71eec7ec0de51522528d36f00"
|
|
251
|
+
dependencies = [
|
|
252
|
+
"log",
|
|
253
|
+
]
|
|
254
|
+
|
|
255
|
+
[[package]]
|
|
256
|
+
name = "windows-targets"
|
|
257
|
+
version = "0.48.5"
|
|
258
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
259
|
+
checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
|
|
260
|
+
dependencies = [
|
|
261
|
+
"windows_aarch64_gnullvm",
|
|
262
|
+
"windows_aarch64_msvc",
|
|
263
|
+
"windows_i686_gnu",
|
|
264
|
+
"windows_i686_msvc",
|
|
265
|
+
"windows_x86_64_gnu",
|
|
266
|
+
"windows_x86_64_gnullvm",
|
|
267
|
+
"windows_x86_64_msvc",
|
|
268
|
+
]
|
|
269
|
+
|
|
270
|
+
[[package]]
|
|
271
|
+
name = "windows_aarch64_gnullvm"
|
|
272
|
+
version = "0.48.5"
|
|
273
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
274
|
+
checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
|
|
275
|
+
|
|
276
|
+
[[package]]
|
|
277
|
+
name = "windows_aarch64_msvc"
|
|
278
|
+
version = "0.48.5"
|
|
279
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
280
|
+
checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
|
|
281
|
+
|
|
282
|
+
[[package]]
|
|
283
|
+
name = "windows_i686_gnu"
|
|
284
|
+
version = "0.48.5"
|
|
285
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
286
|
+
checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
|
|
287
|
+
|
|
288
|
+
[[package]]
|
|
289
|
+
name = "windows_i686_msvc"
|
|
290
|
+
version = "0.48.5"
|
|
291
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
292
|
+
checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
|
|
293
|
+
|
|
294
|
+
[[package]]
|
|
295
|
+
name = "windows_x86_64_gnu"
|
|
296
|
+
version = "0.48.5"
|
|
297
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
298
|
+
checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
|
|
299
|
+
|
|
300
|
+
[[package]]
|
|
301
|
+
name = "windows_x86_64_gnullvm"
|
|
302
|
+
version = "0.48.5"
|
|
303
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
304
|
+
checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
|
|
305
|
+
|
|
306
|
+
[[package]]
|
|
307
|
+
name = "windows_x86_64_msvc"
|
|
308
|
+
version = "0.48.5"
|
|
309
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
310
|
+
checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
[package]
|
|
2
|
+
name = "vizibridge"
|
|
3
|
+
version = "0.1.0"
|
|
4
|
+
edition = "2021"
|
|
5
|
+
|
|
6
|
+
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
|
7
|
+
[lib]
|
|
8
|
+
name = "vizibridge"
|
|
9
|
+
crate-type = ["cdylib"]
|
|
10
|
+
|
|
11
|
+
[dependencies]
|
|
12
|
+
pyo3 = "0.20.0"
|
|
13
|
+
seq-macro = "0.3.5"
|
|
14
|
+
vizitig-lib = { git = "https://gitlab.inria.fr/cpaperma/vizicomp.git" }
|
vizibridge-0.1.0/LICENSE
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
MIT License
|
|
2
|
+
|
|
3
|
+
Copyright (c) 2024 PAPERMAN Charles
|
|
4
|
+
|
|
5
|
+
Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
6
|
+
of this software and associated documentation files (the "Software"), to deal
|
|
7
|
+
in the Software without restriction, including without limitation the rights
|
|
8
|
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
9
|
+
copies of the Software, and to permit persons to whom the Software is
|
|
10
|
+
furnished to do so, subject to the following conditions:
|
|
11
|
+
|
|
12
|
+
The above copyright notice and this permission notice shall be included in all
|
|
13
|
+
copies or substantial portions of the Software.
|
|
14
|
+
|
|
15
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
16
|
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
17
|
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
18
|
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
19
|
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
20
|
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
|
21
|
+
SOFTWARE.
|
|
@@ -0,0 +1,11 @@
|
|
|
1
|
+
Metadata-Version: 2.3
|
|
2
|
+
Name: vizibridge
|
|
3
|
+
Version: 0.1.0
|
|
4
|
+
Classifier: Programming Language :: Rust
|
|
5
|
+
Classifier: Programming Language :: Python :: Implementation :: CPython
|
|
6
|
+
Classifier: Programming Language :: Python :: Implementation :: PyPy
|
|
7
|
+
Requires-Dist: ruff
|
|
8
|
+
Requires-Dist: mypy
|
|
9
|
+
Requires-Dist: pytest
|
|
10
|
+
License-File: LICENSE
|
|
11
|
+
Requires-Python: >=3.8
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["maturin>=1.5,<2.0"]
|
|
3
|
+
build-backend = "maturin"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "vizibridge"
|
|
7
|
+
requires-python = ">=3.8"
|
|
8
|
+
classifiers = [
|
|
9
|
+
"Programming Language :: Rust",
|
|
10
|
+
"Programming Language :: Python :: Implementation :: CPython",
|
|
11
|
+
"Programming Language :: Python :: Implementation :: PyPy",
|
|
12
|
+
]
|
|
13
|
+
dynamic = ["version"]
|
|
14
|
+
|
|
15
|
+
dependencies=[
|
|
16
|
+
"ruff",
|
|
17
|
+
"mypy",
|
|
18
|
+
"pytest"
|
|
19
|
+
]
|
|
20
|
+
|
|
21
|
+
[tool.maturin]
|
|
22
|
+
python-source = "python"
|
|
23
|
+
module-name = "vizibridge._vizibridge"
|
|
24
|
+
features = ["pyo3/extension-module"]
|
|
@@ -0,0 +1,43 @@
|
|
|
1
|
+
from vizibridge._vizibridge import DNA as rust_DNA
|
|
2
|
+
import re
|
|
3
|
+
from typing import Iterator, Self
|
|
4
|
+
|
|
5
|
+
non_CGTA = re.compile("[^ACGT]")
|
|
6
|
+
|
|
7
|
+
class DNA:
|
|
8
|
+
__slots__ = ("data",)
|
|
9
|
+
def __init__(self, data: rust_DNA | str):
|
|
10
|
+
if isinstance(data, str):
|
|
11
|
+
self.data = rust_DNA(data)
|
|
12
|
+
elif isinstance(data, rust_DNA):
|
|
13
|
+
self.data = data
|
|
14
|
+
else:
|
|
15
|
+
raise TypeError(type(data))
|
|
16
|
+
|
|
17
|
+
@classmethod
|
|
18
|
+
def from_str(cls, seq: str) -> Iterator["DNA"]:
|
|
19
|
+
yield from (cls(subseq) for subseq in non_CGTA.split(seq))
|
|
20
|
+
|
|
21
|
+
def __iter__(self) -> Iterator[str]:
|
|
22
|
+
for i in range(len(self.data)):
|
|
23
|
+
self.data.get_index(i)
|
|
24
|
+
|
|
25
|
+
def __getitem__(self, __key: int | slice) -> Self | str:
|
|
26
|
+
if isinstance(__key, int):
|
|
27
|
+
return self.data.get_index(__key)
|
|
28
|
+
if isinstance(__key, slice):
|
|
29
|
+
assert __key.step is None
|
|
30
|
+
data = self.data.get_slice(__key.start, __key.stop)
|
|
31
|
+
return type(self)(data)
|
|
32
|
+
|
|
33
|
+
raise KeyError(__key)
|
|
34
|
+
|
|
35
|
+
def __repr__(self):
|
|
36
|
+
return repr(self.data)
|
|
37
|
+
|
|
38
|
+
|
|
39
|
+
def __len__(self):
|
|
40
|
+
return len(self.data)
|
|
41
|
+
|
|
42
|
+
def enum_canonical_kmer(self, k: int):
|
|
43
|
+
return getattr(self.data, f"enumerate_canonical_kmer{k}")()
|
|
@@ -0,0 +1,107 @@
|
|
|
1
|
+
#![allow(non_local_definitions)]
|
|
2
|
+
use pyo3::prelude::*;
|
|
3
|
+
use pyo3::types::{PyString, PyType};
|
|
4
|
+
use seq_macro::seq;
|
|
5
|
+
use vizitig_lib::dna::{Nucleotid, DNA};
|
|
6
|
+
use vizitig_lib::iterators::CanonicalKmerIterator;
|
|
7
|
+
use vizitig_lib::kmer::ShortKmer;
|
|
8
|
+
|
|
9
|
+
#[pyclass(name = "DNA")]
|
|
10
|
+
pub struct PyDNA {
|
|
11
|
+
pub content: DNA,
|
|
12
|
+
}
|
|
13
|
+
|
|
14
|
+
seq!(N in 3..=31{
|
|
15
|
+
#[pymethods]
|
|
16
|
+
impl PyDNA {
|
|
17
|
+
|
|
18
|
+
#[new]
|
|
19
|
+
pub fn new<'py>(input_pystr: &'py PyString) -> PyResult<Self> {
|
|
20
|
+
let input_str = input_pystr.to_str()?;
|
|
21
|
+
let dna = input_str.as_bytes().try_into().unwrap();
|
|
22
|
+
Ok(PyDNA {
|
|
23
|
+
content: dna
|
|
24
|
+
})
|
|
25
|
+
}
|
|
26
|
+
|
|
27
|
+
pub fn __repr__(&self) -> PyResult<String> {
|
|
28
|
+
Ok(self.content.content.clone().into_iter().map(|u| char::from(u)).collect::<String>())
|
|
29
|
+
}
|
|
30
|
+
|
|
31
|
+
fn __len__(&self) -> PyResult<usize>{
|
|
32
|
+
Ok(self.content.content.len())
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
pub fn get_index(&self, index: usize) -> PyResult<char>{
|
|
36
|
+
Ok(self.content.content[index].into())
|
|
37
|
+
}
|
|
38
|
+
pub fn get_slice(&self, start: usize, stop: usize) -> PyResult<Self> {
|
|
39
|
+
Ok(PyDNA {
|
|
40
|
+
content: DNA {
|
|
41
|
+
content: self.content.content.get(start..stop).unwrap().to_vec()
|
|
42
|
+
}
|
|
43
|
+
})
|
|
44
|
+
}
|
|
45
|
+
|
|
46
|
+
#(
|
|
47
|
+
pub fn enumerate_canonical_kmer~N(&self) -> PyResult<Vec<PyKmer~N>>{
|
|
48
|
+
let it : CanonicalKmerIterator<N, u64> = (&self.content).try_into().unwrap();
|
|
49
|
+
Ok(it.map(|u| PyKmer~N{content: u }).collect())
|
|
50
|
+
}
|
|
51
|
+
)*
|
|
52
|
+
|
|
53
|
+
}
|
|
54
|
+
});
|
|
55
|
+
|
|
56
|
+
seq!(N in 3..=31{
|
|
57
|
+
#[pyclass(name="Kmer")]
|
|
58
|
+
#[derive(Clone)]
|
|
59
|
+
pub struct PyKmer~N{
|
|
60
|
+
content: ShortKmer<N>,
|
|
61
|
+
}
|
|
62
|
+
#[pymethods]
|
|
63
|
+
impl PyKmer~N{
|
|
64
|
+
#[classmethod]
|
|
65
|
+
fn from_dna(_: &PyType, dna: &PyDNA) -> PyResult<Self>{
|
|
66
|
+
let nucleotids : &[Nucleotid; N] = dna.content.content.first_chunk::<N>().unwrap();
|
|
67
|
+
let kmer : ShortKmer<N> = nucleotids.try_into().unwrap();
|
|
68
|
+
Ok(PyKmer~N{ content: kmer })
|
|
69
|
+
}
|
|
70
|
+
|
|
71
|
+
fn add_left_nucleotid(&self, n: char) -> PyResult<Self>{
|
|
72
|
+
Ok(PyKmer~N{ content: self.content.append_left(n.try_into().unwrap()) })
|
|
73
|
+
}
|
|
74
|
+
|
|
75
|
+
|
|
76
|
+
fn add_right_nucleotid(&self, n: char) -> PyResult<Self>{
|
|
77
|
+
Ok(PyKmer~N{ content: self.content.append(n.try_into().unwrap()) })
|
|
78
|
+
}
|
|
79
|
+
|
|
80
|
+
fn __repr__(&self) -> PyResult<String>{
|
|
81
|
+
return Ok(format!("{}", &self.content))
|
|
82
|
+
}
|
|
83
|
+
|
|
84
|
+
fn __str__(&self) -> PyResult<String>{
|
|
85
|
+
return Ok((&self.content).into())
|
|
86
|
+
}
|
|
87
|
+
|
|
88
|
+
fn __lt__(&self, other: Self) -> PyResult<bool> {
|
|
89
|
+
return Ok(self.content <= other.content)
|
|
90
|
+
}
|
|
91
|
+
|
|
92
|
+
fn __gt__(&self, other: Self) -> PyResult<bool> {
|
|
93
|
+
return Ok(self.content >= other.content)
|
|
94
|
+
}
|
|
95
|
+
}
|
|
96
|
+
});
|
|
97
|
+
|
|
98
|
+
|
|
99
|
+
seq!(N in 3..=31{
|
|
100
|
+
#[pymodule]
|
|
101
|
+
fn _vizibridge(_py: Python, m: &PyModule) -> PyResult<()> {
|
|
102
|
+
#(
|
|
103
|
+
m.add_class::<PyKmer~N>()?;
|
|
104
|
+
)*
|
|
105
|
+
m.add_class::<PyDNA>()?;
|
|
106
|
+
Ok(())
|
|
107
|
+
}});
|