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feat: Add a wrapper for quarto markdown rendering #3003

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feat: Add a wrapper for quarto markdown rendering #3003

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50e5a6f
Add a wrapper for quarto markdown rendering
Jun 20, 2024
318edf0
docs: small corrections
Jun 20, 2024
a95864f
doc: improve documentation
Jun 20, 2024
26519a2
doc: improve documentation
Jun 20, 2024
b17f428
Remove renv dependencies from conda env
Jun 21, 2024
9423bd6
Fix meta.yml rendering errors
Jun 21, 2024
98019c4
Add tests for quarto wrapper
Jun 21, 2024
6f5d86b
Pin quarto version
Jun 21, 2024
1ece336
Pin the versions in the test environments
Jun 21, 2024
8a01c7e
Fix wrong folder for quarto tests
Jun 21, 2024
2207ff9
Fix test refering to ../environment.yml
Jun 21, 2024
97e1928
Remove the conda r-dependency example
Jun 22, 2024
3eec186
Merge branch 'master' into feature/quarto
votti Jun 22, 2024
1d1515a
Handle case where not log file defined
Jun 22, 2024
0985231
Add Quarto url
votti Jun 24, 2024
64a7c88
Merge branch 'master' into feature/quarto
votti Jun 27, 2024
efe4687
Merge branch 'master' into feature/quarto
votti Jul 23, 2024
a2b6704
Add tests for resource passing
Jul 8, 2024
3c0a647
Automatically pass resources if named resources_
Jul 23, 2024
7c76c19
Add missing notes section
Jul 29, 2024
aff004e
Fix error quarto has no params
Jul 30, 2024
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125 changes: 122 additions & 3 deletions test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5602,23 +5602,44 @@ def test_ensembl_annotation_gtf_gz():
def test_ensembl_regulatory_gff3_gz():
run(
"bio/reference/ensembl-regulation",
["snakemake", "--cores", "1", "resources/regulatory_features.gff3.gz", "--use-conda", "-F"],
[
"snakemake",
"--cores",
"1",
"resources/regulatory_features.gff3.gz",
"--use-conda",
"-F",
],
)


@skip_if_not_modified
def test_ensembl_regulatory_features_grch37_gff():
run(
"bio/reference/ensembl-regulation",
["snakemake", "--cores", "1", "resources/regulatory_features.gff", "--use-conda", "-F"],
[
"snakemake",
"--cores",
"1",
"resources/regulatory_features.gff",
"--use-conda",
"-F",
],
)


@skip_if_not_modified
def test_ensembl_regulatory_features_mouse_gff_gz():
run(
"bio/reference/ensembl-regulation",
["snakemake", "--cores", "1", "resources/regulatory_features.mouse.gff.gz", "--use-conda", "-F"],
[
"snakemake",
"--cores",
"1",
"resources/regulatory_features.mouse.gff.gz",
"--use-conda",
"-F",
],
)


Expand Down Expand Up @@ -6710,3 +6731,101 @@ def test_emu_combine_output_split():
"-F",
],
)


@skip_if_not_modified
def test_quarto_simple_html():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/simple.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_docx():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/simple.docx",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_parameters():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/example_proj_full.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_noreport():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/example_proj_noreport.txt",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_extra_renv_deps():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/extra_datatable_renv.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_pass_resources():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/resources_custom.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_pass_threads():
run(
"utils/quarto",
[
"snakemake",
"--cores",
"1",
"output/resources_threads.html",
"--use-conda",
],
)
138 changes: 138 additions & 0 deletions utils/quarto/environment.linux-64.pin.txt
View file
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Original file line number Diff line number Diff line change
@@ -0,0 +1,138 @@
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080
https://conda.anaconda.org/conda-forge/linux-64/dart-sass-1.58.3-ha770c72_1.conda#d54982a58cd9be3d00a7efe76ba6f60c
https://conda.anaconda.org/conda-forge/linux-64/esbuild-0.19.2-ha770c72_0.conda#8fa87b764cf6143cb66e9cc3548b186a
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https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
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https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
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https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h3d2ce59_11.conda#c485da4fdb454539f852a90ae06e9bb7
https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_11.conda#eaa8ea74083fb4a78ae19e431e556003
https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814
https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c
https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036
https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08
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https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hd590300_0.conda#b462a33c0be1421532f28bfe8f4a7514
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908
https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852_1002.tar.bz2#06feff3d2634e3097ce2fe681474b534
https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda#bce9f945da8ad2ae9b1d7165a64d0f87
https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15
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https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_11.conda#4c3e460d6acf8e43e4ce8bf405187eb7
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae
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https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123
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channels:
- conda-forge
- nodefaults
dependencies:
- r-quarto=1.4
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