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Add Readthedoc feature #15

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Jun 17, 2024
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3845af3
add readthedoc yaml file
shenvitor Jun 4, 2024
52bbc60
add essential set-up files if using rtd
shenvitor Jun 6, 2024
5e5a047
more essential set-up files if using rtd
shenvitor Jun 6, 2024
3d345c2
directory specification
shenvitor Jun 6, 2024
1f6e247
location rename
shenvitor Jun 6, 2024
95f69ce
install rtd theme
shenvitor Jun 6, 2024
2892baa
rst file
shenvitor Jun 6, 2024
9d6d073
hello
shenvitor Jun 6, 2024
05ebb94
hello world
shenvitor Jun 6, 2024
0ea61f2
yaml file confy file location
shenvitor Jun 6, 2024
a20a5de
adjust to mystnb
shenvitor Jun 7, 2024
99fe394
Adjust configuration for RTD
shenvitor Jun 7, 2024
a5ed974
Ensure _static directory exists
shenvitor Jun 7, 2024
85f269e
add python version in git workflow ci file
shenvitor Jun 7, 2024
b227762
Ensure _static directory exists with a .keep file
shenvitor Jun 7, 2024
1635fc9
make _templates directory exists with a .keep file
shenvitor Jun 7, 2024
6670cf0
update most of the request changes
shenvitor Jun 11, 2024
3b72423
Remove pyproject.toml and rely on pixi.toml
shenvitor Jun 11, 2024
9be9505
Remove requirements.txt and update .readthedoc.yaml
shenvitor Jun 11, 2024
514ea3c
Add build-docs.sh and update .readthedoc.yaml
shenvitor Jun 11, 2024
cead558
update commands in .readthedoc.yaml
shenvitor Jun 11, 2024
9f23541
add custom build steps in .readthedoc.yaml
shenvitor Jun 11, 2024
470bfc9
pixi shell custom build steps in .readthedoc.yaml
shenvitor Jun 11, 2024
9296e67
pixi install custom build steps in .readthedoc.yaml
shenvitor Jun 11, 2024
ecd5520
pixi custom build steps in .readthedoc.yaml
shenvitor Jun 11, 2024
8c789c1
pixi source custom build steps in .readthedoc.yaml
shenvitor Jun 11, 2024
de092ce
pixi source at home folder custom build steps in .readthedoc.yaml
shenvitor Jun 11, 2024
11b18ce
custom build steps in RTD yaml
shenvitor Jun 11, 2024
109788b
pixi location
shenvitor Jun 11, 2024
d50722c
in 1 line
shenvitor Jun 11, 2024
f4d5473
change to command
shenvitor Jun 11, 2024
b7c23f1
change back to build
shenvitor Jun 11, 2024
3872f23
jobs
shenvitor Jun 11, 2024
1066b68
pixi install shell
shenvitor Jun 11, 2024
c764ba7
export
shenvitor Jun 11, 2024
ef82961
remove pixi shell in rtd yaml
shenvitor Jun 11, 2024
13a82a2
modify again in rtd yaml
shenvitor Jun 11, 2024
20d6256
correction again in rtd yaml
shenvitor Jun 11, 2024
276d103
change sphinx in rtd yaml
shenvitor Jun 11, 2024
94c5c4b
move to above in rtd yaml
shenvitor Jun 11, 2024
7085d98
remove commands in rtd yaml
shenvitor Jun 11, 2024
657d996
post_build
shenvitor Jun 11, 2024
3b4f9ad
only essentials in post_install
shenvitor Jun 11, 2024
5b812ce
location update
shenvitor Jun 11, 2024
5d2025d
stucks here
shenvitor Jun 11, 2024
bd5d1e2
add build_commends maybe
shenvitor Jun 11, 2024
dd52c07
again post build maybe
shenvitor Jun 11, 2024
8a9dbde
add back python maybe
shenvitor Jun 11, 2024
e63b382
wrap into post_install
shenvitor Jun 11, 2024
980f254
add pre_biild
shenvitor Jun 12, 2024
8e35409
add install before pre_biild
shenvitor Jun 12, 2024
5523780
try only pixi shell in pre_biild
shenvitor Jun 12, 2024
6a051d7
attempt to run command bypassing the need of an interactive shell in …
shenvitor Jun 12, 2024
e5992b4
only pixi shell and then python
shenvitor Jun 12, 2024
0ca76fa
Add back pyproject again
shenvitor Jun 12, 2024
c2c8b15
remove build-docs.sh
shenvitor Jun 12, 2024
d760eeb
remove pyproject again
shenvitor Jun 12, 2024
f7231ef
update .readthedoc.yaml by an example
shenvitor Jun 17, 2024
5c3746c
reduce diff with main branch
shenvitor Jun 17, 2024
653cd5f
Merge branch 'main' into readthedoc
shenvitor Jun 17, 2024
418daad
remove cell timeout and print traceback
shenvitor Jun 17, 2024
7fee9c9
move html output to RTD location
shenvitor Jun 17, 2024
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15 changes: 15 additions & 0 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
version: "2"

build:
os: "ubuntu-22.04"
tools:
python: "3.12"
jobs:
post_install:
- curl -fsSL https://pixi.sh/install.sh | bash
- export PATH="$HOME/.pixi/bin:$PATH" && pixi install
- pixi shell -c "pixi install && sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html"
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Unfortunately, RTD runs its own sphinx-build command (hence pre_build, post_build, not build itself). So just running pixi shell should suffice 🤞 If it doesn't, this may be a more tricky issue to solve...

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Btw pixi install is not needed, at most pixi shell

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@shenvitor shenvitor Jun 12, 2024

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Unfortunately, RTD runs its own sphinx-build command (hence pre_build, post_build, not build itself). So just running pixi shell should suffice 🤞 If it doesn't, this may be a more tricky issue to solve...

Seems like it doesn't, maybe tricky? What if the pixi shell an interactive shell which is not supported in the ReadTheDocs environment, maybe?

e.g. this issue in RTD build indicates that it probably can't start an interactive shell there:
Screenshot 2024-06-12 at 11 21 22

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sphinx:
builder: html
configuration: docs/conf.py
fail_on_warning: true
3 changes: 3 additions & 0 deletions build-docs.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
#!/bin/sh
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This file can be removed, right?

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yup originally just testing

. $(pixi shell --quiet)
pixi run docnb
29 changes: 26 additions & 3 deletions docs/conf.py
Original file line number Diff line number Diff line change
@@ -1,12 +1,35 @@
project = "GlueX-Nstar"
author = "ComPWA"

exclude_patterns = [
"**.ipynb_checkpoints",
".DS_Store",
".pixi",
"Thumbs.db",
"_build",
]
extensions = ["myst_nb"]
html_theme = "pydata_sphinx_theme"
extensions = [
"myst_nb",
"sphinx.ext.duration",
"sphinx.ext.doctest",
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.intersphinx",
"sphinx.ext.napoleon",
"sphinx.ext.viewcode",
]
html_theme = "sphinx_rtd_theme"
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This theme change is not required on RTD. Also works with what you had before.

master_doc = "index"
myst_enable_extensions = [
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"colon_fence",
"deflist",
"dollarmath",
"html_admonition",
"html_image",
"linkify",
"substitution",
"tasklist",
]
nitpicky = True
project = "GlueX N-Star"
nb_execution_mode = "auto"
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version = "0.1.0"
10 changes: 1 addition & 9 deletions docs/hello.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"id": "0",
"metadata": {},
"source": [
"# Starting document"
"# Hello"
]
},
{
Expand All @@ -17,14 +17,6 @@
"source": [
"print(\"Hello World!\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand Down
10 changes: 9 additions & 1 deletion docs/index.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,12 @@
# MyST-NB Quickstart
# Welcome Page

# Welcome to GlueX-Nstar documentation!

Investigation of the N\* Resonances in the GlueX Experiment

> **Note:** This project is under active development.
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I would use a MyST admonition here


## Contents

```{toctree}
hello
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Expand Down
160 changes: 149 additions & 11 deletions pixi.lock
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.1.1-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.8-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20.1-py312h7900ff3_3.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.4-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.0.1-pyhd8ed1ab_0.conda
Expand Down Expand Up @@ -143,6 +143,7 @@ environments:
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- conda: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/linkify-it-py-2.0.3-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/livereload-2.6.3-pyh9f0ad1d_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-3.0.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.5-py312h98912ed_0.conda
Expand All @@ -156,9 +157,12 @@ environments:
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- conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-3.0.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.4-hd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.4-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.16.4-hd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbdime-4.0.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.4-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.6.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nodeenv-1.8.0-pyhd8ed1ab_0.conda
Expand All @@ -169,6 +173,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/opt_einsum-3.3.0-pyhc1e730c_2.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/overrides-7.7.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-24.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2-ha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/pango-1.52.2-ha41ecd1_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/parso-0.8.4-pyhd8ed1ab_0.conda
Expand Down Expand Up @@ -216,9 +221,11 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.5-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinx-7.3.7-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinx-autobuild-2024.4.16-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-2.0.0-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.8-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.6-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda
Expand All @@ -238,6 +245,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.11.0-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/typing_utils-0.1.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-1.0.3-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/ukkonen-1.0.1-py312h8572e83_4.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.1-pyhd8ed1ab_0.conda
Expand Down Expand Up @@ -835,18 +843,19 @@ packages:
timestamp: 1702383349284
- kind: conda
name: docutils
version: 0.21.2
build: pyhd8ed1ab_0
subdir: noarch
noarch: python
url: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda
sha256: 362bfe3afaac18298c48c0c6a935641544077ce5105a42a2d8ebe750ad07c574
md5: e8cd5d629f65bdf0f3bb312cde14659e
version: 0.20.1
build: py312h7900ff3_3
build_number: 3
subdir: linux-64
url: https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20.1-py312h7900ff3_3.conda
sha256: b9fb75d806afc53d9d7b98edb0c45ac38a3cc983916b8dac4ad7ddac5c18a024
md5: 1b90835ae26b9b8250b302649359a989
depends:
- python >=3.9
- python >=3.12,<3.13.0a0
- python_abi 3.12.* *_cp312
license: CC-PDDC AND BSD-3-Clause AND BSD-2-Clause AND ZPL-2.1
size: 403226
timestamp: 1713930478970
size: 898253
timestamp: 1701882735141
- kind: conda
name: entrypoints
version: '0.4'
Expand Down Expand Up @@ -2684,6 +2693,22 @@ packages:
license_family: Other
size: 61588
timestamp: 1686575217516
- kind: conda
name: linkify-it-py
version: 2.0.3
build: pyhd8ed1ab_0
subdir: noarch
noarch: python
url: https://conda.anaconda.org/conda-forge/noarch/linkify-it-py-2.0.3-pyhd8ed1ab_0.conda
sha256: aa99d44e8c83865026575a8af253141c53e0b3ab05f053befaa7757c8525064f
md5: f1b64ca4faf563605cf6f6ca93f9ff3f
depends:
- python >=3.7
- uc-micro-py
license: MIT
license_family: MIT
size: 24035
timestamp: 1707129321841
- kind: conda
name: livereload
version: 2.6.3
Expand Down Expand Up @@ -2910,6 +2935,22 @@ packages:
license_family: BSD
size: 27851
timestamp: 1710317767117
- kind: conda
name: nbconvert
version: 7.16.4
build: hd8ed1ab_0
subdir: noarch
noarch: generic
url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.4-hd8ed1ab_0.conda
sha256: 7a4a759b8930833cbfffbfd92da069f1d3fd43760ea629c8612b9e7ae9fff0e8
md5: c9d64b8a7ee8e6bdbf0e7d8aa7f39601
depends:
- nbconvert-core 7.16.4 pyhd8ed1ab_0
- nbconvert-pandoc 7.16.4 hd8ed1ab_0
license: BSD-3-Clause
license_family: BSD
size: 8434
timestamp: 1714477296945
- kind: conda
name: nbconvert-core
version: 7.16.4
Expand Down Expand Up @@ -2944,6 +2985,22 @@ packages:
license_family: BSD
size: 189004
timestamp: 1714477286178
- kind: conda
name: nbconvert-pandoc
version: 7.16.4
build: hd8ed1ab_0
subdir: noarch
noarch: generic
url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.16.4-hd8ed1ab_0.conda
sha256: d3bd8b38a74825e9e502f3251fba167b303d7ad324cd4e41d459bfa3c118c9ee
md5: 391934bd1a79990c23df1d1809ddc821
depends:
- nbconvert-core 7.16.4 pyhd8ed1ab_0
- pandoc
license: BSD-3-Clause
license_family: BSD
size: 8479
timestamp: 1714477291801
- kind: conda
name: nbdime
version: 4.0.1
Expand Down Expand Up @@ -2987,6 +3044,27 @@ packages:
license_family: BSD
size: 101232
timestamp: 1712239122969
- kind: conda
name: nbsphinx
version: 0.9.4
build: pyhd8ed1ab_0
subdir: noarch
noarch: python
url: https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.4-pyhd8ed1ab_0.conda
sha256: 2d5756e2ab94ba73d630b97bc8ce6b0ea6eb60aadc2ad7e47e6e6d48fe3f87e8
md5: 9dc80eaeff56fb67dbf4f871b81bc13a
depends:
- docutils
- jinja2
- nbconvert
- nbformat
- python >=3.6
- sphinx
- traitlets
license: MIT
license_family: MIT
size: 33630
timestamp: 1715074950890
- kind: conda
name: ncurses
version: '6.5'
Expand Down Expand Up @@ -3150,6 +3228,18 @@ packages:
license_family: APACHE
size: 49832
timestamp: 1710076089469
- kind: conda
name: pandoc
version: '3.2'
build: ha770c72_0
subdir: linux-64
url: https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2-ha770c72_0.conda
sha256: 418348076c1a39170efb0bdc8a584ddd11e9ed0ff58ccd905488d3f165ca98ba
md5: 8c924f0b7f3e064b1c954a08e7c32fba
license: GPL-2.0-or-later
license_family: GPL
size: 21088628
timestamp: 1715499623651
- kind: conda
name: pandocfilters
version: 1.5.0
Expand Down Expand Up @@ -3953,6 +4043,24 @@ packages:
license_family: MIT
size: 16466
timestamp: 1713319509734
- kind: conda
name: sphinx_rtd_theme
version: 2.0.0
build: pyha770c72_0
subdir: noarch
noarch: python
url: https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-2.0.0-pyha770c72_0.conda
sha256: 8545c806d03092fd0236db6663c88036eab2dc99e34c91cd36c0704db03b148a
md5: baf6d9a33df1a789ca55e3b404c7ea28
depends:
- docutils <0.21
- python >=3.6
- sphinx >=5,<8
- sphinxcontrib-jquery >=4,<5
license: MIT
license_family: MIT
size: 2614217
timestamp: 1701183633165
- kind: conda
name: sphinxcontrib-applehelp
version: 1.0.8
Expand Down Expand Up @@ -4001,6 +4109,21 @@ packages:
license_family: BSD
size: 33499
timestamp: 1705118297318
- kind: conda
name: sphinxcontrib-jquery
version: '4.1'
build: pyhd8ed1ab_0
subdir: noarch
noarch: python
url: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda
sha256: 2e5f16a2d58f9a31443ffbb8ce3852cfccf533a6349045828cd2e994ef0679ca
md5: 914897066d5873acfb13e75705276ad1
depends:
- python >=2.7
- sphinx >=1.8
license: 0BSD AND MIT
size: 112985
timestamp: 1678809100921
- kind: conda
name: sphinxcontrib-jsmath
version: 1.0.1
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license: LicenseRef-Public-Domain
size: 119815
timestamp: 1706886945727
- kind: conda
name: uc-micro-py
version: 1.0.3
build: pyhd8ed1ab_0
subdir: noarch
noarch: python
url: https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-1.0.3-pyhd8ed1ab_0.conda
sha256: 54293cd94da3a6b978b353eb7897555055d925ad0008bc73e85cca19e2587ed0
md5: 3b7fc78d7be7b450952aaa916fb78877
depends:
- python >=3.6
license: MIT
license_family: MIT
size: 11162
timestamp: 1707507514699
- kind: conda
name: ukkonen
version: 1.0.1
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5 changes: 5 additions & 0 deletions pixi.toml
Original file line number Diff line number Diff line change
Expand Up @@ -28,12 +28,17 @@ jupyterlab = ">=4.2.0,<4.3"
jupyterlab-git = ">=0.50.0,<0.51"
jupyterlab-lsp = ">=5.1.0,<5.2"
jupyterlab-myst = ">=2.4.2,<2.5"
linkify-it-py = ">=2.0.3,<2.1"
myst-nb = ">=1.1.0,<1.2"
myst-parser = ">=3.0.1,<3.1"
nbsphinx = ">=0.9.4,<0.10"
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I would use myst-nb instead of nbsphinx (that's a different notebook renderer). That also removes the need for myst-parser, maybe also that linkify-md thing, because those are indirect dependencies of myst-nb

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Actually, why are dependency changes required in this PR?

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I added them when I added RTD from their example

numpy = ">=1.26.4,<1.27"
pre-commit = ">=3.7.1,<3.8"
pydata-sphinx-theme = ">=0.15.2,<0.16"
python = ">=3.12.3,<3.13"
python-graphviz = ">=0.20.3,<0.21"
scipy = ">=1.13.0,<1.14"
sphinx = ">=7.3.7,<7.4"
sphinx-autobuild = ">=2024.4.16,<2024.5"
sphinx_rtd_theme = ">=2.0.0,<2.1"
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Are you selecting that in conf.py?

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Yes I have

sympy = ">=1.12,<2"