Add "user tutorial plus develop" to "develop"

.github/workflows/action.yml

@@ -0,0 +1,29 @@
+name: Documentation URLs Check
+
+on:
+  pull_request:
+  push:
+    branches:
+      - 'release-*'
+      - 'develop'
+      - 'staging'
+      - 'main'
+
+    tags:
+      - 'v*'
+  schedule:
+    # Run everyday at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
+    - cron: "1 2 * * *"
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        base-branch: 'staging'
+        max-depth: -1
+        check-modified-files-only: 'yes'
+        config-file: '.github/workflows/config.json'
+        file-extension: '.md'

.github/workflows/config.json

@@ -0,0 +1,7 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": "^http://docs.github", "^pkgs.org"
+    }
+  ]
+}

.lycheeignore

@@ -0,0 +1,11 @@
+http://update.knime.com/*
+http://update.knime.org/*
+https://github.com/*
+https://pkgs.org/*
+http://docutils*
+https://analyticalsciencejournals.onlinelibrary.wiley.com/*
+https://pubs.acs.org/*
+http://dx.doi.org/*
+https://www.pnas.org/*
+http://pubs.acs.org/*
+https://www.sciencedirect.com/*

.vscode/configurationCache.log

@@ -0,0 +1 @@
+{"buildTargets":[".PHONY","Makefile","all","help"],"launchTargets":[],"customConfigurationProvider":{"workspaceBrowse":{"browsePath":[],"compilerArgs":[]},"fileIndex":[]}}

.vscode/dryrun.log

@@ -0,0 +1,5 @@
+make --dry-run --always-make --keep-going --print-directory
+make: Entering directory `/Users/christinakumar/openms-docs/OpenMS-docs'
+sphinx-build -M help "docs" "build"  
+make: Leaving directory `/Users/christinakumar/openms-docs/OpenMS-docs'
+

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "makefile.extensionOutputFolder": "./.vscode"
+}

.vscode/targets.log

@@ -0,0 +1,258 @@
+make all --print-data-base --no-builtin-variables --no-builtin-rules --question
+# GNU Make 3.81
+# Copyright (C) 2006  Free Software Foundation, Inc.
+# This is free software; see the source for copying conditions.
+# There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+# This program built for i386-apple-darwin11.3.0
+
+
+# Make data base, printed on Thu Aug 18 16:31:51 2022
+
+# Variables
+
+# automatic
+<D = $(patsubst %/,%,$(dir $<))
+# automatic
+?F = $(notdir $?)
+# automatic
+?D = $(patsubst %/,%,$(dir $?))
+# makefile (from `Makefile', line 7)
+SPHINXPROJ = openms
+# automatic
+@D = $(patsubst %/,%,$(dir $@))
+# automatic
+@F = $(notdir $@)
+# makefile
+CURDIR := /Users/christinakumar/openms-docs/OpenMS-docs
+# makefile
+
+SHELL = /bin/sh
+# environment
+VSCODE_NLS_CONFIG = {"locale":"en-us","availableLanguages":{},"_languagePackSupport":true}
+# environment
+_ = /usr/bin/make
+# makefile (from `Makefile', line 1)
+MAKEFILE_LIST :=  Makefile
+# makefile (from `Makefile', line 9)
+BUILDDIR = build
+# environment
+__CFBundleIdentifier = com.microsoft.VSCode
+# environment
+VSCODE_CWD = /
+# environment
+PATH = /Users/christinakumar/.sdkman/candidates/java/current/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/share/dotnet:/opt/X11/bin:~/.dotnet/tools:/Library/Apple/usr/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/Applications/Wireshark.app/Contents/MacOS
+# environment
+SDKMAN_DIR = /Users/christinakumar/.sdkman
+# environment
+SDKMAN_CANDIDATES_API = https://api.sdkman.io/2
+# environment
+SDKMAN_PLATFORM = darwinx64
+# environment
+ELECTRON_RUN_AS_NODE = 1
+# default
+.FEATURES := target-specific order-only second-expansion else-if archives jobserver check-symlink
+# environment
+SSH_AUTH_SOCK = /private/tmp/com.apple.launchd.xOZVLPmn7f/Listeners
+# automatic
+%F = $(notdir $%)
+# environment
+DISPLAY = /private/tmp/com.apple.launchd.PhxnEpIHml/org.xquartz:0
+# environment
+PWD = /Users/christinakumar/openms-docs/OpenMS-docs
+# environment
+ORIGINAL_XDG_CURRENT_DESKTOP = undefined
+# environment
+VSCODE_AMD_ENTRYPOINT = vs/workbench/api/node/extensionHostProcess
+# environment
+HOME = /Users/christinakumar
+# default
+MAKEFILEPATH := /Applications/Xcode.app/Contents/Developer/Makefiles
+# environment
+VSCODE_CODE_CACHE_PATH = /Users/christinakumar/Library/Application Support/Code/CachedData/3b889b090b5ad5793f524b5d1d39fda662b96a2a
+# environment
+LOGNAME = christinakumar
+# environment
+APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL = 1
+# environment
+VSCODE_HANDLES_UNCAUGHT_ERRORS = true
+# automatic
+^D = $(patsubst %/,%,$(dir $^))
+# environment
+XPC_FLAGS = 0x0
+# environment
+SDKMAN_VERSION = 5.15.0
+# default
+MAKE = $(MAKE_COMMAND)
+# default
+MAKECMDGOALS := all
+# environment
+SHLVL = 2
+# environment
+JAVA_HOME = /Users/christinakumar/.sdkman/candidates/java/current
+# default
+MAKE_VERSION := 3.81
+# environment
+USER = christinakumar
+# makefile
+.DEFAULT_GOAL := help
+# automatic
+%D = $(patsubst %/,%,$(dir $%))
+# makefile (from `Makefile', line 5)
+SPHINXOPTS = 
+# default
+MAKE_COMMAND := /Applications/Xcode.app/Contents/Developer/usr/bin/make
+# default
+.VARIABLES := 
+# environment
+TMPDIR = /var/folders/hj/1tg2psn112l93qd9chvzg8bm0000gn/T/
+# automatic
+*F = $(notdir $*)
+# environment
+VSCODE_IPC_HOOK = /Users/christinakumar/Library/Application Support/Code/1.69.2-main.sock
+# environment
+MallocNanoZone = 0
+# makefile
+MAKEFLAGS = Rrqp
+# environment
+MFLAGS = -Rrqp
+# automatic
+*D = $(patsubst %/,%,$(dir $*))
+# environment
+XPC_SERVICE_NAME = application.com.microsoft.VSCode.12929192943.12929192949
+# automatic
++D = $(patsubst %/,%,$(dir $+))
+# makefile (from `Makefile', line 6)
+SPHINXBUILD = sphinx-build
+# automatic
++F = $(notdir $+)
+# environment
+__CF_USER_TEXT_ENCODING = 0x1F5:0x0:0x0
+# environment
+COMMAND_MODE = unix2003
+# default
+MAKEFILES := 
+# automatic
+<F = $(notdir $<)
+# environment
+SDKMAN_CANDIDATES_DIR = /Users/christinakumar/.sdkman/candidates
+# environment
+LC_ALL = C
+# automatic
+^F = $(notdir $^)
+# default
+SUFFIXES := 
+# default
+.INCLUDE_DIRS = /usr/local/include
+# environment
+MAKELEVEL := 0
+# environment
+LANG = C
+# makefile (from `Makefile', line 8)
+SOURCEDIR = docs
+# environment
+VSCODE_PID = 1319
+# variable set hash-table stats:
+# Load=70/1024=7%, Rehash=0, Collisions=1/101=1%
+
+# Pattern-specific Variable Values
+
+# No pattern-specific variable values.
+
+# Directories
+
+# . (device 16777220, inode 12923647332): 18 files, no impossibilities.
+
+# 18 files, no impossibilities in 1 directories.
+
+# Implicit Rules
+
+%: Makefile
+#  commands to execute (from `Makefile', line 21):
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+
+# 1 implicit rules, 0 (0.0%) terminal.
+
+# Files
+
+all: Makefile
+
+#  Command-line target.
+#  Implicit rule search has been done.
+#  Implicit/static pattern stem: `all'
+#  File does not exist.
+#  File has been updated.
+#  Needs to be updated (-q is set).
+# automatic
+# @ := all
+# automatic
+# % := 
+# automatic
+# * := all
+# automatic
+# + := Makefile
+# automatic
+# | := 
+# automatic
+# < := Makefile
+# automatic
+# ^ := Makefile
+# automatic
+# ? := Makefile
+# variable set hash-table stats:
+# Load=8/32=25%, Rehash=0, Collisions=2/16=12%
+#  commands to execute (from `Makefile', line 21):
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+
+.PHONY: help Makefile
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+# Not a target:
+.SUFFIXES:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+Makefile:
+#  Phony target (prerequisite of .PHONY).
+#  Implicit rule search has not been done.
+#  File does not exist.
+#  File has been updated.
+#  Successfully updated.
+
+help:
+#  Phony target (prerequisite of .PHONY).
+#  Implicit rule search has not been done.
+#  File does not exist.
+#  File has not been updated.
+#  commands to execute (from `Makefile', line 13):
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+
+# Not a target:
+.DEFAULT:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+# files hash-table stats:
+# Load=6/1024=1%, Rehash=0, Collisions=0/23=0%
+# VPATH Search Paths
+
+# No `vpath' search paths.
+
+# No general (`VPATH' variable) search path.
+
+# # of strings in strcache: 1
+# # of strcache buffers: 1
+# strcache size: total = 4096 / max = 4096 / min = 4096 / avg = 4096
+# strcache free: total = 4087 / max = 4087 / min = 4087 / avg = 4087
+
+# Finished Make data base on Thu Aug 18 16:31:51 2022
+
+

_ext/pathrole.py

@@ -46,19 +46,19 @@ def make_path_nodes(rawtext, pathparts, app, options):
     except AttributeError:
         raise ValueError('pathicon configuration value is not set')
     #
-    triangle = nodes.inline(text="▹")
+    triangle = nodes.inline(text="▸")
     #triangle = nodes.Text("▹")
     triangle.set_class("pathsep_triangle")
 
     #retnodes = [nodes.image(app.config.pathicon, **options), triangle]
-    nobrhtml = "<nobr>"
+    nobrhtml = "<nobr class='path'>"
     nobrelem = nodes.raw('', nobrhtml, format="html")
     brhtml = "<br>"
     brelem = nodes.raw('', brhtml, format="html")
     nobrhtmlclose = "</nobr>"
     nobrelemclose = nodes.raw('', nobrhtmlclose, format="html")
 
-    html = f"<i class=\"{app.config.pathicon}\"></i>"
+    html = f"<i class=\"{app.config.pathicon} path\"></i>"
     retnodes = [nobrelem, nodes.raw('', html, format="html")]
     for part in pathparts[:-1]:
         if part == "/break":