From 22ccc1ede388bf2be6c3fae3b25db6c4d86723bf Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 11 Sep 2024 09:13:30 +0200 Subject: [PATCH 1/5] Update example-doc.yml --- .github/workflows/example-doc.yml | 34 ++++++++++++++++++++++++++----- 1 file changed, 29 insertions(+), 5 deletions(-) diff --git a/.github/workflows/example-doc.yml b/.github/workflows/example-doc.yml index 96d329b..b5ec52f 100644 --- a/.github/workflows/example-doc.yml +++ b/.github/workflows/example-doc.yml @@ -19,16 +19,40 @@ jobs: - name: Checkout uses: actions/checkout@v4 - - name: Build PDF + - name: Build draft PDF run: >- docker run \ --volume "$(pwd):/data" \ --user "$(id -u):$(id -g)" \ openjournals/inara:latest \ - -o contextpdf example/paper.md + -o "jats,contextpdf,crossref,preprint" example/paper.md - - name: Upload PDF + - name: Upload draft PDF uses: actions/upload-artifact@v3 with: - name: paper - path: example/paper.context.pdf + name: draft + path: | + example/jats/paper.jats + example/paper.context.pdf + example/paper.crossref + example/paper.pdf + example/paper.preprint.tex + + - name: Build production PDF + run: >- + docker run \ + --volume "$(pwd):/data" \ + --user "$(id -u):$(id -g)" \ + openjournals/inara:latest \ + -o "jats,contextpdf,crossref,preprint" -p example/paper.md + + - name: Upload production PDF + uses: actions/upload-artifact@v3 + with: + name: production + path: | + example/jats/paper.jats + example/paper.context.pdf + example/paper.crossref + example/paper.pdf + example/paper.preprint.tex From eb3449aaded65d798bb4211ab84b3aea2659196e Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 11 Sep 2024 09:42:04 +0200 Subject: [PATCH 2/5] Update example-doc.yml --- .github/workflows/example-doc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/example-doc.yml b/.github/workflows/example-doc.yml index b5ec52f..c8a9541 100644 --- a/.github/workflows/example-doc.yml +++ b/.github/workflows/example-doc.yml @@ -25,7 +25,7 @@ jobs: --volume "$(pwd):/data" \ --user "$(id -u):$(id -g)" \ openjournals/inara:latest \ - -o "jats,contextpdf,crossref,preprint" example/paper.md + -o "jats,contextpdf,crossref,preprint,pdf" example/paper.md - name: Upload draft PDF uses: actions/upload-artifact@v3 @@ -44,7 +44,7 @@ jobs: --volume "$(pwd):/data" \ --user "$(id -u):$(id -g)" \ openjournals/inara:latest \ - -o "jats,contextpdf,crossref,preprint" -p example/paper.md + -o "jats,contextpdf,crossref,preprint,pdf" -p example/paper.md - name: Upload production PDF uses: actions/upload-artifact@v3 From f7a614efc5fcfa2d66f8f7422a5a7b0ef46ad1ec Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 11 Sep 2024 09:43:07 +0200 Subject: [PATCH 3/5] Update paper.md --- example/paper.md | 47 +++++++++++++++++++++-------------------------- 1 file changed, 21 insertions(+), 26 deletions(-) diff --git a/example/paper.md b/example/paper.md index 9bb0a33..fa4c36b 100644 --- a/example/paper.md +++ b/example/paper.md @@ -1,19 +1,19 @@ --- title: >- - Article Writing with Markdown and the Open Journals publishing pipeline + Article Writing with Markdown and the Open Journals publishing pipeline authors: - name: Albert Krewinkel email: albert@zeitkraut.de - affiliation: [1, 2, 4] + affiliation: [ 1, 2, 4 ] orcid: 0000-0002-9455-0796 corresponding: true - name: Juanjo Bazán orcid: 0000-0001-7699-3983 - affiliation: [1] + affiliation: [ 1 ] equal-contrib: true - name: Arfon M. Smith orcid: 0000-0002-3957-2474 - affiliation: [1, 3] + affiliation: [ 1, 3 ] equal-contrib: true affiliations: - index: 1 @@ -53,7 +53,6 @@ paper by @upper1974. [YAML]: https://yaml.org - # Statement of Need The journal publisher, in most cases where you'd be reading this, Open @@ -84,21 +83,21 @@ The markup in Markdown should be semantic, not presentations. The table below gives a small example. +---------------------+-------------------------+-----------------------+ -| Markup | Markdown example | Rendered output | +| Markup | Markdown example | Rendered output | +:====================+:=======================:+:=====================:+ -| emphasis | `*this*` | *this* | +| emphasis | `*this*` | *this* | +---------------------+-------------------------+-----------------------+ -| strong emphasis | `**that**` | **that** | +| strong emphasis | `**that**` | **that** | +---------------------+-------------------------+-----------------------+ -| strikeout | `~~not this~~` | ~~not this~~ | +| strikeout | `~~not this~~` | ~~not this~~ | +---------------------+-------------------------+-----------------------+ -| subscript | `H~2~O` | H~2~O | +| subscript | `H~2~O` | H~2~O | +---------------------+-------------------------+-----------------------+ -| superscript | `Ca^2+^` | Ca^2+^ | +| superscript | `Ca^2+^` | Ca^2+^ | +---------------------+-------------------------+-----------------------+ -| underline | `[underline]{.ul}` | [underline]{.ul} | +| underline | `[underline]{.ul}` | [underline]{.ul} | +---------------------+-------------------------+-----------------------+ -| inline code | `` `return 23` `` | `return 23` | +| inline code | `` `return 23` `` | `return 23` | +---------------------+-------------------------+-----------------------+ : Basic inline markup and examples. @@ -138,8 +137,7 @@ can sometimes be useful to give images an explicit height and/or width, e.g. when adding an image as part of a paragraph. The Markdown `![Nyan cat](nyan-cat.png){height="9pt"}` includes the image "nyan-cat.png" ![Nyan cat](images/nyan-cat.png){height="9pt"} while scaling it to a height of -9 pt. - +9 pt. ![The "Mandrill" standard test image, sometimes erroneously called "Baboon", is a popular sample photo and used in image processing @@ -199,7 +197,7 @@ can be any sequence of characters, like `[^marker]`, but may not contain whitespace characters. [^markers]: Although it should be noted that some publishers prefer - symbols or letters as footnote markers. +symbols or letters as footnote markers. The above example results in the following output: @@ -208,7 +206,6 @@ The above example results in the following output: > > [^1]: An open license that allows reuse. - ## Blocks The larger components of a document are called "blocks". @@ -241,7 +238,6 @@ discouraged. Usually [lists], as described in the next section, should be preferred over forth- and fifth-level headings. - ### Lists Bullet lists and numbered lists, a.k.a. enumerations, offer an @@ -256,8 +252,8 @@ additional method to present sequential and hierarchical information. - apples - citrus fruits - - lemons - - oranges + - lemons + - oranges Enumerations start with the number of the first item. Using the the first two [laws of @@ -282,7 +278,6 @@ Rendered: gained as heat, $Q$, less the thermodynamic work, $W$, done by the system on its surroundings. $$\Delta U = Q - W$$ - # Article metadata ## Names @@ -422,13 +417,13 @@ number of the referenced float. E.g., in this document `\ref{proglangs}` gives "\ref{proglangs}". : Comparison of programming languages used in the publishing tool. - []{label="proglangs"} +[]{label="proglangs"} -| Language | Typing | Garbage Collected | Evaluation | Created | +| Language | Typing | Garbage Collected | Evaluation | Created | |----------|:---------------:|:-----------------:|------------|---------| -| Haskell | static, strong | yes | non-strict | 1990 | -| Lua | dynamic, strong | yes | strict | 1993 | -| C | static, weak | no | strict | 1972 | +| Haskell | static, strong | yes | non-strict | 1990 | +| Lua | dynamic, strong | yes | strict | 1993 | +| C | static, weak | no | strict | 1972 | ## Equations From 362677dffe0356fc9f9d80a085020adbe36d61c8 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 16 Sep 2024 12:57:41 +0200 Subject: [PATCH 4/5] Revert --- example/paper.md | 46 +++++++++++++++++++++++++--------------------- 1 file changed, 25 insertions(+), 21 deletions(-) diff --git a/example/paper.md b/example/paper.md index fa4c36b..043882b 100644 --- a/example/paper.md +++ b/example/paper.md @@ -1,19 +1,19 @@ --- title: >- - Article Writing with Markdown and the Open Journals publishing pipeline + Article Writing with Markdown and the Open Journals publishing pipeline authors: - name: Albert Krewinkel email: albert@zeitkraut.de - affiliation: [ 1, 2, 4 ] + affiliation: [1, 2, 4] orcid: 0000-0002-9455-0796 corresponding: true - name: Juanjo Bazán orcid: 0000-0001-7699-3983 - affiliation: [ 1 ] + affiliation: [1] equal-contrib: true - name: Arfon M. Smith orcid: 0000-0002-3957-2474 - affiliation: [ 1, 3 ] + affiliation: [1, 3] equal-contrib: true affiliations: - index: 1 @@ -83,21 +83,21 @@ The markup in Markdown should be semantic, not presentations. The table below gives a small example. +---------------------+-------------------------+-----------------------+ -| Markup | Markdown example | Rendered output | +| Markup | Markdown example | Rendered output | +:====================+:=======================:+:=====================:+ -| emphasis | `*this*` | *this* | +| emphasis | `*this*` | *this* | +---------------------+-------------------------+-----------------------+ -| strong emphasis | `**that**` | **that** | +| strong emphasis | `**that**` | **that** | +---------------------+-------------------------+-----------------------+ -| strikeout | `~~not this~~` | ~~not this~~ | +| strikeout | `~~not this~~` | ~~not this~~ | +---------------------+-------------------------+-----------------------+ -| subscript | `H~2~O` | H~2~O | +| subscript | `H~2~O` | H~2~O | +---------------------+-------------------------+-----------------------+ -| superscript | `Ca^2+^` | Ca^2+^ | +| superscript | `Ca^2+^` | Ca^2+^ | +---------------------+-------------------------+-----------------------+ -| underline | `[underline]{.ul}` | [underline]{.ul} | +| underline | `[underline]{.ul}` | [underline]{.ul} | +---------------------+-------------------------+-----------------------+ -| inline code | `` `return 23` `` | `return 23` | +| inline code | `` `return 23` `` | `return 23` | +---------------------+-------------------------+-----------------------+ : Basic inline markup and examples. @@ -137,7 +137,8 @@ can sometimes be useful to give images an explicit height and/or width, e.g. when adding an image as part of a paragraph. The Markdown `![Nyan cat](nyan-cat.png){height="9pt"}` includes the image "nyan-cat.png" ![Nyan cat](images/nyan-cat.png){height="9pt"} while scaling it to a height of -9 pt. +9 pt. + ![The "Mandrill" standard test image, sometimes erroneously called "Baboon", is a popular sample photo and used in image processing @@ -197,7 +198,7 @@ can be any sequence of characters, like `[^marker]`, but may not contain whitespace characters. [^markers]: Although it should be noted that some publishers prefer -symbols or letters as footnote markers. + symbols or letters as footnote markers. The above example results in the following output: @@ -206,6 +207,7 @@ The above example results in the following output: > > [^1]: An open license that allows reuse. + ## Blocks The larger components of a document are called "blocks". @@ -238,6 +240,7 @@ discouraged. Usually [lists], as described in the next section, should be preferred over forth- and fifth-level headings. + ### Lists Bullet lists and numbered lists, a.k.a. enumerations, offer an @@ -252,8 +255,8 @@ additional method to present sequential and hierarchical information. - apples - citrus fruits - - lemons - - oranges + - lemons + - oranges Enumerations start with the number of the first item. Using the the first two [laws of @@ -278,6 +281,7 @@ Rendered: gained as heat, $Q$, less the thermodynamic work, $W$, done by the system on its surroundings. $$\Delta U = Q - W$$ + # Article metadata ## Names @@ -417,13 +421,13 @@ number of the referenced float. E.g., in this document `\ref{proglangs}` gives "\ref{proglangs}". : Comparison of programming languages used in the publishing tool. -[]{label="proglangs"} + []{label="proglangs"} -| Language | Typing | Garbage Collected | Evaluation | Created | +| Language | Typing | Garbage Collected | Evaluation | Created | |----------|:---------------:|:-----------------:|------------|---------| -| Haskell | static, strong | yes | non-strict | 1990 | -| Lua | dynamic, strong | yes | strict | 1993 | -| C | static, weak | no | strict | 1972 | +| Haskell | static, strong | yes | non-strict | 1990 | +| Lua | dynamic, strong | yes | strict | 1993 | +| C | static, weak | no | strict | 1972 | ## Equations From ca35a99ae2bd1592b0433b0845cf6d8e8ae14026 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 16 Sep 2024 15:28:17 +0200 Subject: [PATCH 5/5] Update example-doc.yml --- .github/workflows/example-doc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/example-doc.yml b/.github/workflows/example-doc.yml index 114457c..c4c3362 100644 --- a/.github/workflows/example-doc.yml +++ b/.github/workflows/example-doc.yml @@ -45,7 +45,7 @@ jobs: --volume "$(pwd):/data" \ --user "$(id -u):$(id -g)" \ openjournals/inara:latest \ - -o "jats,contextpdf,crossref,preprint,pdf" -p example/paper.md + -o "jats,contextpdf,crossref,preprint,tex,pdf" -p example/paper.md - name: Upload production PDF uses: actions/upload-artifact@v3