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feat: Add a wrapper for quarto markdown rendering #3003

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98 changes: 98 additions & 0 deletions test.py
Original file line number Diff line number Diff line change
Expand Up @@ -6686,3 +6686,101 @@ def test_emu_combine_output_split():
"-F",
],
)


@skip_if_not_modified
def test_quarto_simple_html():
run(
"bio/emu/combine-outputs",
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[
"snakemake",
"--cores",
"1",
"output/simple.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_html():
run(
"bio/emu/combine-outputs",
[
"snakemake",
"--cores",
"1",
"output/simple.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_docx():
run(
"bio/emu/combine-outputs",
[
"snakemake",
"--cores",
"1",
"output/simple.docx",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_parameters():
run(
"bio/emu/combine-outputs",
[
"snakemake",
"--cores",
"1",
"output/example_proj_full.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_noreport():
run(
"bio/emu/combine-outputs",
[
"snakemake",
"--cores",
"1",
"output/example_proj_noreport.txt",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_extra_conda_deps():
run(
"bio/emu/combine-outputs",
[
"snakemake",
"--cores",
"1",
"output/extra_datatable_conda.html",
"--use-conda",
],
)


@skip_if_not_modified
def test_quarto_simple_extra_renv_deps():
run(
"bio/emu/combine-outputs",
[
"snakemake",
"--cores",
"1",
"output/extra_datatable_renv.html",
"--use-conda",
],
)
138 changes: 138 additions & 0 deletions utils/quarto/environment.linux-64.pin.txt
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
https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
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https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74
https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-hdb50d1a_111.conda#43178c27fac2dcd495bd9e58e18272d9
https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hdb50d1a_111.conda#4ffa92ea4ba6555dee156ce3d0ae7a9b
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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
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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
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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/deno-dom-0.1.35-hd9586b0_1.conda#263ee0870b18b013d9ec8539113ac69f
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https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.conda#93ee23f12bc2e684548181256edd2cf6
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda#9653f1bf3766164d0e65fa723cabbc54
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https://conda.anaconda.org/conda-forge/linux-64/r-askpass-1.2.0-r43h57805ef_0.conda#ee095f1d72a1d80864816e44623ba392
https://conda.anaconda.org/conda-forge/linux-64/r-cachem-1.1.0-r43hb1dbf0f_0.conda#d48720030e2b1d780389bafa5a9c7536
https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r43h57805ef_2.conda#10c5892991072cfa3a61489d2ac6ad66
https://conda.anaconda.org/conda-forge/noarch/r-highr-0.11-r43hc72bb7e_0.conda#ecd3b95a01caa7bdcf63714427b5b88c
https://conda.anaconda.org/conda-forge/linux-64/r-later-1.3.2-r43ha503ecb_0.conda#6e120827a341f21444881e84408e98a7
https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r43hc72bb7e_0.conda#291d2fb68ea1b181644b40d6743ae000
https://conda.anaconda.org/conda-forge/linux-64/r-pki-0.1_14-r43hb1dbf0f_0.conda#58c4dc882730c0d96ca09e58be0150d8
https://conda.anaconda.org/conda-forge/linux-64/r-processx-3.8.4-r43h57805ef_0.conda#660d4e9ff8beef35dbda645484d17a25
https://conda.anaconda.org/conda-forge/noarch/r-tinytex-0.51-r43hc72bb7e_0.conda#16653f65f1ab934e1a9bdac874f9b63b
https://conda.anaconda.org/conda-forge/linux-64/r-htmltools-0.5.8.1-r43ha503ecb_0.conda#220b9c45f5867a42d49bde8d340e9e53
https://conda.anaconda.org/conda-forge/noarch/r-knitr-1.47-r43hc72bb7e_0.conda#0310660d998a5933bb4545a312ed7385
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https://conda.anaconda.org/conda-forge/noarch/r-jquerylib-0.1.4-r43hc72bb7e_2.conda#49a3fad710cbccec9139b36587842f88
https://conda.anaconda.org/conda-forge/noarch/r-rsconnect-1.3.1-r43hc72bb7e_0.conda#474409574da3aacf988008567cbf11b7
https://conda.anaconda.org/conda-forge/linux-64/r-sass-0.4.9-r43ha503ecb_0.conda#58e32ad6d979828aa0fc3da59e1b4d78
https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.7.0-r43hc72bb7e_0.conda#6e2bfdc782284259390d09bb083142b2
https://conda.anaconda.org/conda-forge/noarch/r-rmarkdown-2.27-r43hc72bb7e_1.conda#4b681e35650d7d10737bc0c6ed80ae9a
https://conda.anaconda.org/conda-forge/noarch/r-quarto-1.4-r43hc72bb7e_0.conda#a86d89513116deba7cc3c6e8e72a0f61
5 changes: 5 additions & 0 deletions utils/quarto/environment.yaml
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channels:
- conda-forge
- nodefaults
dependencies:
- r-quarto=1.4
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