diff --git a/README.md b/README.md index 1f4007fdf4..5c4e42b2d6 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ - - - Nextflow Logo + + + Nextflow Logo *"Dataflow variables are spectacularly expressive in concurrent programming"* diff --git a/docs/images/dag.mmd b/docs/_static/dag.mmd similarity index 100% rename from docs/images/dag.mmd rename to docs/_static/dag.mmd diff --git a/docs/_static/degular/Degular-Bold.woff b/docs/_static/degular/Degular-Bold.woff new file mode 100644 index 0000000000..189e5c40ef Binary files /dev/null and b/docs/_static/degular/Degular-Bold.woff differ diff --git a/docs/_static/degular/Degular-Bold.woff2 b/docs/_static/degular/Degular-Bold.woff2 new file mode 100644 index 0000000000..5f49fd7355 Binary files /dev/null and b/docs/_static/degular/Degular-Bold.woff2 differ diff --git a/docs/_static/degular/Degular-BoldItalic.woff b/docs/_static/degular/Degular-BoldItalic.woff new file mode 100644 index 0000000000..164d8a58ce Binary files /dev/null and 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0000000000..99a758d21a --- /dev/null +++ b/docs/_static/seqera-logo.svg @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + diff --git a/docs/_static/theme.css b/docs/_static/theme.css index 27d788d7e8..f4fc4528b3 100644 --- a/docs/_static/theme.css +++ b/docs/_static/theme.css @@ -1,22 +1,172 @@ +/* Inter font */ +@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;700&display=swap'); -/* navbar -- Seqera logo */ +/* Degular font */ +@font-face { + font-family: "Degular"; + src: url('degular/Degular-Regular.woff2'); + src: url('degular/Degular-Regular.woff2') format('woff2'), + url('degular/Degular-Regular.woff') format('woff'); + font-weight: normal; + font-style: normal; +} +@font-face { + font-family: "Degular"; + src: url('degular/Degular-Italic.woff2'); + src: url('degular/Degular-Italic.woff2') format('woff2'), + url('degular/Degular-Italic.woff') format('woff'); + font-weight: normal; + font-style: italic; +} +@font-face { + font-family: "Degular"; + src: url('degular/Degular-Bold.woff2'); + src: url('degular/Degular-Bold.woff2') format('woff2'), + url('degular/Degular-Bold.woff') format('woff'); + font-weight: bold; + font-style: normal; +} +@font-face { + font-family: "Degular"; + src: url('degular/Degular-BoldItalic.woff2'); + src: url('degular/Degular-BoldItalic.woff2') format('woff2'), + url('degular/Degular-BoldItalic.woff') format('woff'); + font-weight: bold; + font-style: italic; +} -.wy-side-nav-search { - background-color: #27ae60; +/* fonts */ +body { + font-family: 'Inter', sans-serif; +} + +.btn { + font-family: 'Inter', sans-serif; +} + +.rst-content .toctree-wrapper>p.caption, +h1, +h2, +h3, +h4, +h5, +h6, +legend { + font-family: 'Degular', sans-serif; +} + +/* colors */ +.rst-content .danger { + background: #FEEDEC; +} + +.rst-content .danger .admonition-title { + background: #C3514D; +} + +.rst-content .warning { + background: #FDF0E9; +} + +.rst-content .warning .admonition-title { + background: #BC6437; +} + +.rst-content .note { + background: #E8F2FF; +} + +.rst-content .note .admonition-title { + background: #3787E5; +} + +.rst-content .tip { + background: #E2F7F3; +} + +.rst-content .tip .admonition-title { + background: #0CAE8E; +} + +a, a:visited { + color: #3787E5; } +a:hover { + color: #77B5FE; +} + +.rst-content code, +.rst-content tt, +code { + color: #C3514D; +} + +.wy-menu-vertical header, .wy-menu-vertical p.caption { - color: #27ae60; + color: #0DC09D; +} + +.wy-menu-vertical a { + color: #EAEBEB; +} + +.wy-menu-vertical a:hover { + background-color: #7B7B7B; } .wy-menu-vertical a:active { - background-color: #27ae60; + background-color: #0DC09D; +} + +.wy-side-nav-search { + background-color: #0DC09D; +} + +.wy-side-nav-search input[type=text] { + border-color: #0DC09D; +} + +.wy-side-nav-search img { + background-color: #0DC09D; +} + +.wy-nav-side { + background: #160F26; +} + +.wy-nav-top { + background: #0DC09D; +} + +.wy-nav-top a { + color: #fff; +} + +.wy-nav-top img { + width: auto; + background-color: inherit; + border-radius: unset; +} + +footer { + color: #7B7B7B; +} + +#search-results .context { + color: #7B7B7B; +} + +.rst-content code.literal, +.rst-content tt.literal { + color: #C3514D; } +/* Custom footer with logo */ .nav-footer-logo { width: 300px; margin-top: 2rem; - border-top: 1px solid #666666; + border-top: 1px solid #7B7B7B; text-align: center; font-size: 80%; } @@ -24,7 +174,7 @@ .nav-footer-logo a { display: block; padding: 2rem 0 0.5rem; - color: #666666; + color: #7B7B7B; } .nav-footer-logo a img { @@ -33,7 +183,9 @@ } /* Version change admonitions */ -div.deprecated, div.versionadded, div.versionchanged { +div.deprecated, +div.versionadded, +div.versionchanged { border-left: 0.2rem solid; border-radius: 0.25rem; box-shadow: 0 0.2rem 0.5rem var(--pst-color-shadow),0 0 0.0625rem var(--pst-color-shadow)!important; @@ -45,11 +197,15 @@ div.deprecated, div.versionadded, div.versionchanged { transition: color .25s,background-color .25s,border-color .25s; vertical-align: middle; } -div.deprecated>p, div.versionadded>p, div.versionchanged>p { +div.deprecated>p, +div.versionadded>p, +div.versionchanged>p { margin-top: 0.5rem; margin-bottom: 0.5rem; } -div.deprecated>p:first-child::before, div.versionadded>p:first-child::before, div.versionchanged>p:first-child::before { +div.deprecated>p:first-child::before, +div.versionadded>p:first-child::before, +div.versionchanged>p:first-child::before { font-family: FontAwesome; display: inline-block; font-style: normal; @@ -62,9 +218,9 @@ div.deprecated>p:first-child::before, div.versionadded>p:first-child::before, di padding: 0.4rem 0.6rem; margin: -0.2rem 0rem -0.2rem -0.6rem; } -div.versionadded { border-color: #1abc9c; background-color: #dbfaf4; } -div.versionadded p:first-child::before { color: #1abc9c; } -div.versionchanged { border-color: #f0b37e; background-color: #ffedcc; } -div.versionchanged p:first-child::before { color: #f0b37e; } -div.deprecated { border-color: #f29f97; background-color: #fdf3f2; } -div.deprecated p:first-child::before { color: #f29f97; } +div.versionadded { border-color: #0CAE8E; background-color: #E2F7F3; } +div.versionadded p:first-child::before { color: #0CAE8E; } +div.versionchanged { border-color: #BC6437; background-color: #FDF0E9; } +div.versionchanged p:first-child::before { color: #BC6437; } +div.deprecated { border-color: #C3514D; background-color: #FEEDEC; } +div.deprecated p:first-child::before { color: #C3514D; } diff --git a/docs/images/timeline-min.png b/docs/_static/timeline-min.png similarity index 100% rename from docs/images/timeline-min.png rename to docs/_static/timeline-min.png diff --git a/docs/images/workflow-notification-min.png b/docs/_static/workflow-notification-min.png similarity index 100% rename from docs/images/workflow-notification-min.png rename to docs/_static/workflow-notification-min.png diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html index b08dd9ff4e..af1d87ad40 100644 --- a/docs/_templates/layout.html +++ b/docs/_templates/layout.html @@ -5,7 +5,7 @@ {% endblock %} diff --git a/docs/conf.py b/docs/conf.py index 142e2f76ba..4591e86d00 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -92,7 +92,7 @@ #show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = 'default' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] @@ -136,12 +136,12 @@ # The name of an image file (relative to this directory) to place at the top # of the sidebar. -html_logo = 'images/nextflow-logo.png' +html_logo = '_static/nextflow-logo.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -html_favicon = 'images/favicon.ico' +html_favicon = '_static/favicon.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, @@ -217,7 +217,7 @@ # The name of an image file (relative to this directory) to place at the top of # the title page. -latex_logo = 'images/nextflow-logo.png' +latex_logo = '_static/nextflow-logo.png' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. diff --git a/docs/images/favicon.ico b/docs/images/favicon.ico deleted file mode 100644 index ed7fa1ee70..0000000000 Binary files a/docs/images/favicon.ico and /dev/null differ diff --git a/docs/images/nextflow-logo.png b/docs/images/nextflow-logo.png deleted file mode 100644 index 3eb4d8c0c0..0000000000 Binary files a/docs/images/nextflow-logo.png and /dev/null differ diff --git a/docs/images/yourkit.png b/docs/images/yourkit.png deleted file mode 100644 index b973fb1518..0000000000 Binary files a/docs/images/yourkit.png and /dev/null differ diff --git a/docs/kubernetes.md b/docs/kubernetes.md index 06c954d55f..e6f38a9542 100644 --- a/docs/kubernetes.md +++ b/docs/kubernetes.md @@ -16,7 +16,7 @@ Kubernetes abstracts also the storage provisioning through the definition of one When using the `k8s` executor Nextflow deploys the workflow execution as a Kubernetes pod. This pod orchestrates the workflow execution and submits a separate pod execution for each job that need to be carried out by the workflow application. -```{image} /images/nextflow-k8s-min.png +```{image} _static/nextflow-k8s-min.png ``` ## Requirements diff --git a/docs/mail.md b/docs/mail.md index 4ada1916f5..59ce19890a 100644 --- a/docs/mail.md +++ b/docs/mail.md @@ -183,7 +183,7 @@ nextflow run -N It will send a notification mail when the execution completes similar to the one shown below: -```{image} images/workflow-notification-min.png +```{image} _static/workflow-notification-min.png ``` :::{warning} diff --git a/docs/metrics.md b/docs/metrics.md index 694d68cd05..0681328ab6 100644 --- a/docs/metrics.md +++ b/docs/metrics.md @@ -8,7 +8,7 @@ This section details how the resource usage metrics from the {ref}`Execution rep The plot reports how much CPU resources were used by each process. -```{image} images/report-resource-cpu.png +```{image} _static/report-resource-cpu.png ``` Let's illustrate how this plot behaves with several examples. @@ -248,17 +248,17 @@ process bar { The `Virtual (RAM + Disk swap)` tab shows that both `foo` and `bar` processes use the same amount of virtual memory (~1 GiB): -```{image} images/report-resource-memory-vmem.png +```{image} _static/report-resource-memory-vmem.png ``` However, the `Physical (RAM)` tab shows that only the `bar` process uses ~1 GiB of RAM while `foo` process uses ~0 GiB: -```{image} images/report-resource-memory-ram.png +```{image} _static/report-resource-memory-ram.png ``` As expected, the `% RAM Allocated` tab shows that 0% of the resource set in the `memory` directive was used for `foo` process while 67% (= 1 / 1.5) of the resource were used for `bar` process: -```{image} images/report-resource-memory-pctram.png +```{image} _static/report-resource-memory-pctram.png ``` :::{warning} @@ -269,7 +269,7 @@ Memory and storage metrics are reported in bytes. This means that 1KB = $1024$ b The plot has two tabs the job duration (a.k.a. elapsed real time, real time or wall time ) in the `Raw Usage` tag and the percentage of requested time used in the `% Allocated` tab with respect to the duration set in the `time` directive of the process. -```{image} images/report-resource-job-duration.png +```{image} _static/report-resource-job-duration.png ``` ## I/O Usage @@ -294,10 +294,10 @@ process io_read_write_256M { `Read` tab: -```{image} images/report-resource-io-read.png +```{image} _static/report-resource-io-read.png ``` `Write` tab: -```{image} images/report-resource-io-write.png +```{image} _static/report-resource-io-write.png ``` diff --git a/docs/tracing.md b/docs/tracing.md index 32326098a5..0a2a2911a7 100644 --- a/docs/tracing.md +++ b/docs/tracing.md @@ -109,7 +109,7 @@ The report file name can be specified as an optional parameter following the rep The `Summary` section reports the execution status, the launch command, overall execution time and some other workflow metadata. You can see an example below: -```{image} images/report-summary-min.png +```{image} _static/report-summary-min.png ``` ### Resource Usage @@ -118,7 +118,7 @@ The `Resources` section plots the distribution of resource usage for each workfl Plots are shown for CPU, memory, job duration and disk I/O. They have two (or three) tabs with the raw values and a percentage representation showing what proportion of the requested resources were used. These plots are very helpful to check that task resources are used efficiently. -```{image} images/report-resource-cpu.png +```{image} _static/report-resource-cpu.png ``` Learn more about how resource usage is computed in the {ref}`Metrics documentation `. @@ -129,7 +129,7 @@ Learn more about how resource usage is computed in the {ref}`Metrics documentati The `Tasks` section lists all executed tasks, reporting for each of them the status, the actual command script, and many other metrics. You can see an example below: -```{image} images/report-tasks-min.png +```{image} _static/report-tasks-min.png ``` :::{note} @@ -326,7 +326,7 @@ Please read {ref}`Trace scope ` section to learn more about it. Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the timeline report is shown below: -```{image} images/timeline-min.png +```{image} _static/timeline-min.png ``` Each bar represents a process run in the pipeline execution. The bar length represents the task duration time (wall-time). The colored area in each bar represents the real execution time. The grey area to the *left* of the colored area represents the task scheduling wait time. The grey area to the *right* of the colored area represents the task termination time (clean-up and file un-staging). The numbers on the x-axis represent the time in absolute units e.g. minutes, hours, etc. @@ -402,5 +402,5 @@ Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://git nextflow run rnaseq-nf -preview -with-dag ``` -```{mermaid} images/dag.mmd +```{mermaid} _static/dag.mmd ``` diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy index b242a3533d..7cc351048f 100644 --- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy @@ -206,7 +206,7 @@ class WorkflowNotifier { * @return A {@link Attachment} object representing the image logo to be included in the HTML email */ protected Attachment loadDefaultLogo() { - Attachment.resource('/nextflow/mail/nextflow200x40.png', contentId: '', disposition: 'inline') + Attachment.resource('/nextflow/mail/nextflow-logo-v2-min.png', contentId: '', disposition: 'inline') } private String loadDefaultTemplate0(String classpathResource) { diff --git a/modules/nextflow/src/main/resources/nextflow/mail/nextflow-logo-v2-min.png b/modules/nextflow/src/main/resources/nextflow/mail/nextflow-logo-v2-min.png new file mode 100644 index 0000000000..20ca91afb0 Binary files /dev/null and b/modules/nextflow/src/main/resources/nextflow/mail/nextflow-logo-v2-min.png differ diff --git a/modules/nextflow/src/main/resources/nextflow/mail/nextflow200x40.png b/modules/nextflow/src/main/resources/nextflow/mail/nextflow200x40.png deleted file mode 100644 index f91037bbd9..0000000000 Binary files a/modules/nextflow/src/main/resources/nextflow/mail/nextflow200x40.png and /dev/null differ diff --git a/modules/nextflow/src/main/resources/nextflow/mail/notification.html b/modules/nextflow/src/main/resources/nextflow/mail/notification.html index 96eadfea4b..736630e248 100644 --- a/modules/nextflow/src/main/resources/nextflow/mail/notification.html +++ b/modules/nextflow/src/main/resources/nextflow/mail/notification.html @@ -139,7 +139,7 @@

Execution summary

- + This email was sent by Nextflow
cite doi:10.1038/nbt.3820
http://nextflow.io
diff --git a/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html b/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html index 7232373fdd..9d3fe8cf96 100644 --- a/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html +++ b/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html @@ -93,7 +93,7 @@