MACROS

CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS

Info about macros

Macros Plugin Environment

General List

All available variables and filters within the macros plugin:

Variable	Type	Content
extra	dict
config	MkDocsConfig	{'config_file_path': '/home/runner/work/eri-support-docs/eri-support-docs/mkdocs.yml', 'site_name': 'eRI Support Documentation', 'nav': None, 'pages': None, 'exclude_docs': None, 'draft_docs': None, 'not_in_nav': None, 'site_url': 'https://mattbixley.github.io/eri-support-docs/', 'site_description': 'eRI Support Documentation', 'site_author': None, 'theme': Theme(name='material', dirs=['/home/runner/work/eri-support-docs/eri-support-docs/overrides', '/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/material/templates', '/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/mkdocs/templates'], static_templates={'sitemap.xml', '404.html'}, name='material', locale=Locale('en'), language='en', direction=None, features=['navigation.indexes', 'navigation.instant', 'navigation.instant.prefetch', 'navigation.top', 'navigation.tracking', 'navigation.path', 'content.code.copy', 'content.action.edit', 'header.site_name_homepage'], font={'text': 'Roboto', 'code': 'Roboto Mono'}, icon=None, favicon='assets/icons/favicon.ico', logo='assets/icons/logo.svg', palette=[{'primary': 'custom', 'scheme': 'default', 'toggle': {'icon': 'material/lightbulb', 'name': 'Switch to dark mode'}}, {'primary': 'custom', 'scheme': 'slate', 'toggle': {'icon': 'material/lightbulb-outline', 'name': 'Switch to light mode'}}]), 'docs_dir': '/home/runner/work/eri-support-docs/eri-support-docs/docs', 'site_dir': '/home/runner/work/eri-support-docs/eri-support-docs/public', 'copyright': None, 'google_analytics': None, 'dev_addr': _IpAddressValue(host='127.0.0.1', port=8000), 'use_directory_urls': True, 'repo_url': 'https://github.com/MattBixley/eri-support-docs', 'repo_name': 'GitHub', 'edit_uri_template': None, 'edit_uri': 'edit/main/docs/', 'extra_css': ['assets/stylesheets/neoteroi-mkdocs.css', 'assets/stylesheets/footer.css', 'assets/stylesheets/custom_admonations.css', 'assets/stylesheets/theme.css'], 'extra_javascript': ['assets/javascripts/general.js', 'https://status.nesi.org.nz/embed/script.js', 'js/open_in_new_tab.js'], 'extra_templates': [], 'markdown_extensions': ['toc', 'tables', 'fenced_code', 'admonition', 'pymdownx.details', 'pymdownx.superfences', 'pymdownx.highlight', 'pymdownx.inlinehilite', 'pymdownx.tabbed', 'pymdownx.snippets', 'attr_list', 'abbr', 'neoteroi.cards', 'neoteroi.timeline', 'footnotes'], 'mdx_configs': {'toc': {'baselevel': 1, 'permalink': True, 'toc_depth': 3, 'title': 'On this page'}, 'pymdownx.tabbed': {'alternate_style': True}}, 'strict': False, 'remote_branch': 'gh-pages', 'remote_name': 'origin', 'extra': {}, 'plugins': {'material/search': , 'open-in-new-tab': , 'redirects': , 'awesome-pages': , 'material/tags': , 'git-revision-date-localized': , 'macros': , 'mkdocs_hooks.py': }, 'hooks': {'mkdocs_hooks.py': }, 'watch': [], 'validation': {'nav': {'omitted_files': 20, 'not_found': 30, 'absolute_links': 20}, 'links': {'not_found': 30, 'absolute_links': 20, 'unrecognized_links': 20, 'anchors': 20}}}
environment	dict	system = 'Linux', system_version = '6.5.0-1025-azure', python_version = '3.12.7', mkdocs_version = '1.6.0', macros_plugin_version = '1.0.5', jinja2_version = '3.1.3'
plugin	LegacyConfig	{'module_name': 'macro_hooks', 'modules': [], 'render_by_default': True, 'include_dir': 'overrides', 'include_yaml': [], 'j2_block_start_string': '', 'j2_block_end_string': '', 'j2_variable_start_string': '', 'j2_variable_end_string': '', 'on_undefined': 'keep', 'on_error_fail': True, 'verbose': False}
git	dict	status = True, date [datetime], short_commit = '2d39735', commit = '2d39735fdcef5f37e1b3644d6bba5f4d5cb18ba1', tag = '', short_tag = '', author = 'Matt Bixley', author_email = 'mattbixley72@gmail.com', committer = 'GitHub', committer_email = 'noreply@github.com', date_ISO = 'Thu Oct 17 14:53:41 2024 +1300', message = 'Merge pull request #2 from MattBixley/resonant-panther\n\nResonant panther', raw = 'commit 2d39735fdcef5f37e1b3644d6bba5f4d5cb18ba1\nMerge: e537d18 d39c5bc\nAuthor: Matt Bixley \nDate: Thu Oct 17 14:53:41 2024 +1300\n\n Merge pull request #2 from MattBixley/resonant-panther\n \n Resonant panther', root_dir = '/home/runner/work/eri-support-docs/eri-support-docs'
applications	dict	ABAQUS [dict], ABRicate [dict], ABySS [dict], ACTC [dict], ADAM [dict], AGAT [dict], AGE [dict], AMOS [dict], AMRFinderPlus [dict], ANIcalculator [dict], ANNOVAR [dict], ANSYS [dict], ANTLR [dict], ANTs [dict], AOCC [dict], AOCL-BLIS [dict], AOCL-FFTW [dict], AOCL-ScaLAPACK [dict], APR [dict], APR-util [dict], ARCSI [dict], ARIBA [dict], ASAGI [dict], ATK [dict], AUGUSTUS [dict], Abseil [dict], AdapterRemoval [dict], AdaptiveCpp [dict], Advisor [dict], AlphaFold [dict], AlphaFold2DB [dict], AlwaysIntelMKL [dict], Amber [dict], Anaconda3 [dict], Anaconda3-Geo [dict], Anaconda3-Geo2 [dict], Anaconda3_Geo2 [dict], Apptainer [dict], Armadillo [dict], Arrow [dict], Aspera-CLI [dict], Augustus [dict], AutoDock-GPU [dict], AutoDock_Vina [dict], Autoconf-archive [dict], BBMap [dict], BCFtools [dict], BCL-Convert [dict], BEAST [dict], BEDOPS [dict], BEDTools [dict], BEEF [dict], BGC-Bayesian-genomic-clines [dict], BLASR [dict], BLAST [dict], BLASTDB [dict], BLAT [dict], BLIS [dict], BOLT-LMM [dict], BRAKER [dict], BUSCO [dict], BWA [dict], BamTools [dict], Bandage [dict], Basilisk [dict], BayPass [dict], BayeScan [dict], BayesAss [dict], Bazel [dict], Beagle [dict], BerkeleyGW [dict], Berkeley_UPC [dict], BiG-SCAPE [dict], Bifrost [dict], Bio-DB-BigFile [dict], Bio-DB-HTS [dict], BioConductor [dict], BioPP [dict], Bismark [dict], Bison [dict], BlenderPy [dict], Boost [dict], Bowtie [dict], Bowtie2 [dict], Bpipe [dict], Bracken [dict], BreakDancer [dict], BreakSeq2 [dict], CCL [dict], CD-HIT [dict], CDO [dict], CFITSIO [dict], CGAL [dict], CMake [dict], CNVnator [dict], CNVpytor [dict], COMSOL [dict], CONCOCT [dict], CP2K [dict], CPMD [dict], CRAMINO [dict], CTPL [dict], CUDA [dict], CUnit [dict], Cannoli [dict], Canu [dict], CapnProto [dict], Catch2 [dict], CellRanger [dict], Centrifuge [dict], Cereal [dict], CheckM [dict], CheckM2 [dict], CheckV [dict], Circlator [dict], Circos [dict], Clair3 [dict], Clang [dict], Clustal-Omega [dict], ClustalW2 [dict], Corset [dict], CoverM [dict], CppUnit [dict], CubeGUI [dict], CubeLib [dict], CubeWriter [dict], Cufflinks [dict], Cytoscape [dict], D-Genies [dict], DAS_Tool [dict], DB [dict], DBG2OLC [dict], DBus [dict], DFT-D4 [dict], DIAMOND [dict], DISCOVARdenovo [dict], DMTCP [dict], DRAM [dict], DaliLite [dict], DeconSeq [dict], DeePMD-kit [dict], DeepLabCut [dict], Delft3D [dict], Delft3D_FM [dict], Delly [dict], DendroPy [dict], Dorado [dict], Doxygen [dict], Dsuite [dict], EDTA [dict], EIGENSOFT [dict], ELPA [dict], EMAN [dict], EMAN2 [dict], EMBOSS [dict], EMIRGE [dict], ENMTML [dict], ESMF [dict], ETE [dict], EasyBuild [dict], Eigen [dict], Elmer [dict], Embree [dict], EnergyPlus [dict], ErlangOTP [dict], EukRep-EukCC [dict], ExaBayes [dict], ExaML [dict], ExpansionHunter [dict], Extrae [dict], FALCON [dict], FASTX-Toolkit [dict], FCM [dict], FDS [dict], FFTW [dict], FFTW.MPI [dict], FFmpeg [dict], FIGARO [dict], FLTK [dict], FPM [dict], FTGL [dict], FastANI [dict], FastME [dict], FastQC [dict], FastQ_Screen [dict], FastTree [dict], File-Rename [dict], Filtlong [dict], FimTyper [dict], FlexiBLAS [dict], Flye [dict], FoX [dict], FragGeneScan [dict], FreeBayes [dict], FreeSurfer [dict], FreeXL [dict], FriBidi [dict], GATK [dict], GCC [dict], GCCcore [dict], GD [dict], GDAL [dict], GEMMA [dict], GEOS [dict], GLM [dict], GLPK [dict], GLib [dict], GLibmm [dict], GLnexus [dict], GMAP-GSNAP [dict], GMP [dict], GOLD [dict], GObject-Introspection [dict], GPAW [dict], GRASS [dict], GRIDSS [dict], GROMACS [dict], GSL [dict], GST-plugins-base [dict], GStreamer [dict], GTDB-Tk [dict], GTK+ [dict], GTS [dict], GUSHR [dict], Gaussian [dict], Gdk-Pixbuf [dict], GeneMark-ES [dict], GenoVi [dict], GenomeThreader [dict], Gerris [dict], GetOrganelle [dict], GlimmerHMM [dict], Go [dict], Graphviz [dict], Gubbins [dict], Guile [dict], HDF [dict], HDF5 [dict], HISAT2 [dict], HMMER [dict], HMMER2 [dict], HOPS [dict], HTSeq [dict], HTSlib [dict], HarfBuzz [dict], HpcGridRunner [dict], Humann [dict], HybPiper [dict], Hypre [dict], ICU [dict], IDBA [dict], IDBA-UD [dict], IGV [dict], IMPUTE [dict], IQ-TREE [dict], IQmol [dict], IRkernel [dict], ISA-L [dict], IVE [dict], ImageMagick [dict], Infernal [dict], Inspector [dict], InterProScan [dict], JAGS [dict], JUnit [dict], JasPer [dict], Java [dict], Jellyfish [dict], JsonCpp [dict], Julia [dict], JupyterHub [dict], JupyterLab [dict], KAT [dict], KEALib [dict], KMC [dict], Kaiju [dict], Kent_tools [dict], KmerGenie [dict], KorfSNAP [dict], Kraken2 [dict], KronaTools [dict], KyotoCabinet [dict], LAME [dict], LAMMPS [dict], LAST [dict], LASTZ [dict], LDC [dict], LEfSe [dict], LINKS [dict], LLVM [dict], LMDB [dict], LSD2 [dict], LTR_retriever [dict], LUMPY [dict], LZO [dict], LegacySystemLibs [dict], LibTIFF [dict], Libav [dict], Libint [dict], Liftoff [dict], LittleCMS [dict], Loki [dict], LongStitch [dict], M4 [dict], MAFFT [dict], MAGMA [dict], MAKER [dict], MATIO [dict], MATLAB [dict], MCL [dict], MCR [dict], MEGAHIT [dict], METABOLIC [dict], METIS [dict], MMseqs2 [dict], MOB-suite [dict], MODFLOW [dict], MPFR [dict], MPICH [dict], MSMC [dict], MUMPS [dict], MUMmer [dict], MUSCLE [dict], MUST [dict], MaSuRCA [dict], Magma [dict], Mamba [dict], MarkerMiner [dict], Mash [dict], MashMap [dict], Maven [dict], MaxBin [dict], Meraculous [dict], Merqury [dict], Mesa [dict], Meson [dict], MetaBAT [dict], MetaEuk [dict], MetaGeneAnnotator [dict], MetaPhlAn [dict], MetaPhlAn2 [dict], MetaSV [dict], MetaVelvet [dict], Metashape [dict], Metaxa2 [dict], MiMiC [dict], MiMiC-CommLib [dict], Miniconda3 [dict], Miniforge3 [dict], Minimac3 [dict], Minimac4 [dict], MitoZ [dict], ModDotPlot [dict], ModelTest-NG [dict], Molcas [dict], Molpro [dict], Mono [dict], Monocle3 [dict], Mothur [dict], MotionCorr [dict], MrBayes [dict], MultiQC [dict], NAMD [dict], NASM [dict], NCARG [dict], NCCL [dict], NCL [dict], NCO [dict], NECAT [dict], NGS [dict], NLopt [dict], NONMEM [dict], NSPR [dict], NSS [dict], NVHPC [dict], NWChem [dict], NanoComp [dict], NanoLyse [dict], NanoPlot [dict], NanoStat [dict], NewHybrids [dict], Newton-X [dict], NextGenMap [dict], Nextflow [dict], Nim [dict], Ninja [dict], Nsight-Compute [dict], Nsight-Systems [dict], OBITools [dict], OMA [dict], OPARI2 [dict], ORCA [dict], OSPRay [dict], OSU-Micro-Benchmarks [dict], OTF2 [dict], Octave [dict], Octopus [dict], OpenBLAS [dict], OpenBabel [dict], OpenCMISS [dict], OpenCV [dict], OpenFAST [dict], OpenFOAM [dict], OpenJPEG [dict], OpenMPI [dict], OpenSSL [dict], OpenSees [dict], OpenSeesPy [dict], OpenSlide [dict], OrfM [dict], OrthoFiller [dict], OrthoFinder [dict], OrthoMCL [dict], PALEOMIX [dict], PAML [dict], PAPI [dict], PBJelly [dict], PCRE [dict], PCRE2 [dict], PDT [dict], PEAR [dict], PEST++ [dict], PETSc [dict], PFFT [dict], PGI [dict], PHASIUS [dict], PLINK [dict], PLUMED [dict], PRANK [dict], PROJ [dict], PSpaMM [dict], PUMI [dict], Pango [dict], ParMETIS [dict], ParaView [dict], Parallel [dict], ParallelIO [dict], Paraver [dict], Peregrine [dict], Perl [dict], PhyML [dict], PhyloPhlAn [dict], Pilon [dict], PnetCDF [dict], Porechop [dict], Porechop_ABI [dict], PostgreSQL [dict], Prodigal [dict], ProtHint [dict], Proteinortho [dict], PyOpenGL [dict], PyQt [dict], PyTorch [dict], Python [dict], Python-GPU [dict], Python-Geo [dict], QChem [dict], QIIME2 [dict], QUAST [dict], Qt5 [dict], QuantumESPRESSO [dict], QuickTree [dict], R [dict], R-Geo [dict], R-bundle-Bioconductor [dict], RANGS-GSHHS [dict], RAxML [dict], RAxML-NG [dict], RDP-Classifier [dict], RE2 [dict], RECON [dict], REViewer [dict], RFPlasmid [dict], RFdiffusion [dict], RMBlast [dict], RNAmmer [dict], ROCm [dict], ROOT [dict], RSEM [dict], RSGISLib [dict], RStudio-Server [dict], Racon [dict], Ragout [dict], RapidNJ [dict], Ratatosk [dict], Raven [dict], Rcorrector [dict], Relion [dict], RepeatMasker [dict], RepeatModeler [dict], RepeatScout [dict], Riskscape [dict], Roary [dict], Rose [dict], Rosetta [dict], Rstudio [dict], Ruby [dict], Rust [dict], SAGE [dict], SAMtools [dict], SAS [dict], SCOTCH [dict], SCons [dict], SDL2 [dict], SEPP [dict], SHAPEIT4 [dict], SIONlib [dict], SIP [dict], SKESA [dict], SMRT-Link [dict], SNVoter [dict], SNVoter-NanoMethPhase [dict], SOAPdenovo2 [dict], SOCI [dict], SPAdes [dict], SPIDER [dict], SQLite [dict], SSAHA2 [dict], STAR [dict], STAR-Fusion [dict], SUNDIALS [dict], SURVIVOR [dict], SWIG [dict], Salmon [dict], Sambamba [dict], ScaLAPACK [dict], Scalasca [dict], Score-P [dict], SeisSol [dict], SeqAn [dict], SeqAn3 [dict], SeqKit [dict], SeqMonk [dict], SiBELia [dict], Siesta [dict], Siesta-Optical [dict], SignalP [dict], Singularity [dict], Sniffles [dict], SortMeRNA [dict], SourceTracker [dict], Spack [dict], Spark [dict], SpectrA [dict], SqueezeMeta [dict], Stacks [dict], StringTie [dict], Structure [dict], Subread [dict], Subversion [dict], SuiteSparse [dict], SuperLU [dict], Supernova [dict], Szip [dict], TEtranscripts [dict], TMHMM [dict], TOGA [dict], TSEBRA [dict], TURBOMOLE [dict], TWL-NINJA [dict], Tcl [dict], TensorBoard [dict], TensorFlow [dict], TensorRT [dict], Theano [dict], Tk [dict], TopHat [dict], TransDecoder [dict], Transrate [dict], TreeMix [dict], Trilinos [dict], TrimGalore [dict], Trimmomatic [dict], Trinity [dict], Trinotate [dict], Trycycler [dict], TuiView [dict], TurboVNC [dict], UCC [dict], UCX [dict], UDUNITS [dict], USEARCH [dict], Unicycler [dict], VASP [dict], VCF-kit [dict], VCFtools [dict], VEP [dict], VIBRANT [dict], VMD [dict], VSEARCH [dict], VTK [dict], VTune [dict], Valgrind [dict], VarScan [dict], Velvet [dict], VelvetOptimiser [dict], ViennaRNA [dict], Vim [dict], VirHostMatcher [dict], VirSorter [dict], VirtualGL [dict], WAAFLE [dict], WhatsHap [dict], Winnowmap [dict], Wise2 [dict], XALT [dict], XGKS [dict], XHMM [dict], XMDS2 [dict], XSD [dict], XZ [dict], Xerces-C++ [dict], YAXT [dict], Yade [dict], Yasm [dict], Z3 [dict], ZeroMQ [dict], Zip [dict], Zonation [dict], abritamr [dict], angsd [dict], ant [dict], antiSMASH [dict], any2fasta [dict], argtable [dict], aria2 [dict], arpack-ng [dict], at-spi2-atk [dict], at-spi2-core [dict], attr [dict], azul-zulu [dict], bamUtil [dict], barrnap [dict], bcl2fastq2 [dict], beagle-lib [dict], best [dict], binutils [dict], bioawk [dict], blasr_libcpp [dict], branches [dict], breseq [dict], bsddb3 [dict], bzip2 [dict], c-ares [dict], cURL [dict], cairo [dict], cdbfasta [dict], chainforge [dict], chewBBACA [dict], chopper [dict], code-server [dict], compleasm [dict], cromwell [dict], ctags [dict], ctffind [dict], cuDNN [dict], cutadapt [dict], cuteSV [dict], cwltool [dict], cylc [dict], cyvcf2 [dict], dadi [dict], dammit [dict], datamash [dict], datasets [dict], deepTools [dict], devtools [dict], double-conversion [dict], drep [dict], dtcmp [dict], duphold [dict], duplex-tools [dict], eDNA [dict], easi [dict], ecCodes [dict], ectyper [dict], edlib [dict], eggnog-mapper [dict], emmtyper [dict], ensmallen [dict], entrez-direct [dict], exonerate [dict], expat [dict], fastStructure [dict], fastp [dict], fastq-tools [dict], fcGENE [dict], fgbio [dict], fineRADstructure [dict], fineSTRUCTURE [dict], flatbuffers [dict], flex [dict], fmlrc [dict], fmt [dict], fontconfig [dict], forge [dict], foss [dict], freetype [dict], funcx-endpoint [dict], fxtract [dict], g2clib [dict], g2lib [dict], ga4gh [dict], gcloud [dict], geany [dict], gemmforge [dict], genometools [dict], gettext [dict], gfastats [dict], gffread [dict], giflib [dict], gimkl [dict], gimpi [dict], git [dict], globus-automate-client [dict], globus-compute-endpoint [dict], gmsh [dict], gnuplot [dict], gompi [dict], google-sparsehash [dict], googletest [dict], gperf [dict], grib_api [dict], grive2 [dict], gsort [dict], h5pp [dict], haplocheck [dict], help2man [dict], hifiasm [dict], hooks [dict], hunspell [dict], hwloc [dict], hypothesis [dict], icc [dict], iccifort [dict], ifort [dict], iimpi [dict], imkl [dict], imkl-FFTW [dict], impalajit [dict], impi [dict], info [dict], intel [dict], intel-compilers [dict], intltool [dict], iofbf [dict], iompi [dict], ipyrad [dict], ispc [dict], jbigkit [dict], jcvi [dict], jemalloc [dict], jq [dict], json-c [dict], jvarkit [dict], kalign2 [dict], kallisto [dict], kineto [dict], kma [dict], libFLAME [dict], libGLU [dict], libKML [dict], libStatGen [dict], libaec [dict], libarchive [dict], libcircle [dict], libconfig [dict], libdeflate [dict], libdrm [dict], libdwarf [dict], libepoxy [dict], libevent [dict], libffi [dict], libgcrypt [dict], libgd [dict], libgeotiff [dict], libgit2 [dict], libglvnd [dict], libgpg-error [dict], libgpuarray [dict], libgtextutils [dict], libiconv [dict], libjpeg-turbo [dict], libmatheval [dict], libpciaccess [dict], libpmi [dict], libpng [dict], libreadline [dict], libsigc++ [dict], libspatialite [dict], libtool [dict], libunistring [dict], libunwind [dict], libvdwxc [dict], libxc [dict], libxml++ [dict], libxml2 [dict], libxslt [dict], libxsmm [dict], libzstd [dict], lighttpd [dict], likwid [dict], logs [dict], lp_solve [dict], lwgrp [dict], lz4 [dict], maf_stream [dict], magma [dict], make [dict], manta [dict], mapDamage [dict], meRanTK [dict], medaka [dict], megalodon [dict], metaWRAP [dict], miRDeep2 [dict], mimalloc [dict], miniBUSCO [dict], miniasm [dict], minieigen [dict], minimap2 [dict], miniprot [dict], mlpack [dict], modbam2bed [dict], modkit [dict], mosdepth [dict], motif [dict], mpcci [dict], mpifileutils [dict], muParser [dict], nano [dict], nanoQC [dict], nanofilt [dict], nanoget [dict], nanomath [dict], nanopolish [dict], ncbi-vdb [dict], ncurses [dict], ncview [dict], ne [dict], nearline [dict], netCDF [dict], netCDF-C++ [dict], netCDF-C++4 [dict], netCDF-Fortran [dict], nettle [dict], networkx [dict], nodejs [dict], nseg [dict], nsync [dict], nullarbor [dict], numactl [dict], objects [dict], ont-guppy-gpu [dict], openseespy [dict], padloc [dict], pairtools [dict], panaroo [dict], pandoc [dict], parallel [dict], parallel-fastq-dump [dict], parasail [dict], patchelf [dict], pauvre [dict], pggb [dict], pgge [dict], phyx [dict], picard [dict], pigz [dict], pixman [dict], pkg-config [dict], pod5 [dict], pplacer [dict], preseq [dict], prodigal [dict], prodigal-gv [dict], prokka [dict], proovread [dict], protobuf [dict], protobuf-python [dict], psmc [dict], pstoedit [dict], pullseq [dict], purge_dups [dict], purge_haplotigs [dict], pv [dict], pyani [dict], pycoQC [dict], pymol-open-source [dict], pyseer [dict], pyspoa [dict], qcat [dict], rDock [dict], randfold [dict], rasusa [dict], razers3 [dict], rclone [dict], re2c [dict], refs [dict], rkcommon [dict], rnaQUAST [dict], rstudio [dict], rstudio-server [dict], rust-fmlrc [dict], samblaster [dict], samclip [dict], savvy [dict], sbt [dict], sc-RNA [dict], screen_assembly [dict], seqmagick [dict], seqtk [dict], shrinkwrap [dict], simuG [dict], sismonr [dict], slow5tools [dict], smafa [dict], smoove [dict], snakemake [dict], snaphu [dict], snappy [dict], snp-sites [dict], snpEff [dict], somalier [dict], spaln [dict], spdlog [dict], spglib [dict], splat [dict], spoa [dict], sratoolkit [dict], srun-wrapper [dict], sublime [dict], swarm [dict], swissknife [dict], tRNAscan-SE [dict], tabix [dict], tabixpp [dict], tbb [dict], tbl2asn [dict], test [dict], tmux [dict], trf [dict], trimAl [dict], unimap [dict], unrar [dict], util-linux [dict], vcflib [dict], verkko [dict], vg [dict], wgsim [dict], wheel [dict], wtdbg [dict], wxWidgets [dict], x264 [dict], x265 [dict], xbitmaps [dict], xkbcommon [dict], xtb [dict], yacrd [dict], yajl [dict], yak [dict], yaml-cpp [dict], zlib [dict], zstd [dict]
macros	SuperDict	context [function], macros_info [function], now [function], fix_url [function]
filters	dict	pretty [function]
filters_builtin	dict	abs [builtin_function_or_method], attr [function], batch [function], capitalize [function], center [function], count [builtin_function_or_method], d [function], default [function], dictsort [function], e [builtin_function_or_method], escape [builtin_function_or_method], filesizeformat [function], first [function], float [function], forceescape [function], format [function], groupby [function], indent [function], int [function], join [function], last [function], length [builtin_function_or_method], list [function], lower [function], items [function], map [function], min [function], max [function], pprint [function], random [function], reject [function], rejectattr [function], replace [function], reverse [function], round [function], safe [function], select [function], selectattr [function], slice [function], sort [function], string [builtin_function_or_method], striptags [function], sum [function], title [function], trim [function], truncate [function], unique [function], upper [function], urlencode [function], urlize [function], wordcount [function], wordwrap [function], xmlattr [function], tojson [function]
navigation	Navigation
files	Files
page	Page	Page(title='MACROS', url='/eri-support-docs/MACROS/')

Config Information

Standard MkDocs configuration information. Do not try to modify.

e.g. {{ config.docs_dir }}

See also the MkDocs documentation on the config object.

Variable	Type	Content
config_file_path	str	'/home/runner/work/eri-support-docs/eri-support-docs/mkdocs.yml'
site_name	str	'eRI Support Documentation'
nav	NoneType	None
pages	NoneType	None
exclude_docs	NoneType	None
draft_docs	NoneType	None
not_in_nav	NoneType	None
site_url	str	'https://mattbixley.github.io/eri-support-docs/'
site_description	str	'eRI Support Documentation'
site_author	NoneType	None
theme	Theme	Theme(name='material', dirs=['/home/runner/work/eri-support-docs/eri-support-docs/overrides', '/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/material/templates', '/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/mkdocs/templates'], static_templates={'sitemap.xml', '404.html'}, name='material', locale=Locale('en'), language='en', direction=None, features=['navigation.indexes', 'navigation.instant', 'navigation.instant.prefetch', 'navigation.top', 'navigation.tracking', 'navigation.path', 'content.code.copy', 'content.action.edit', 'header.site_name_homepage'], font={'text': 'Roboto', 'code': 'Roboto Mono'}, icon=None, favicon='assets/icons/favicon.ico', logo='assets/icons/logo.svg', palette=[{'primary': 'custom', 'scheme': 'default', 'toggle': {'icon': 'material/lightbulb', 'name': 'Switch to dark mode'}}, {'primary': 'custom', 'scheme': 'slate', 'toggle': {'icon': 'material/lightbulb-outline', 'name': 'Switch to light mode'}}])
docs_dir	str	'/home/runner/work/eri-support-docs/eri-support-docs/docs'
site_dir	str	'/home/runner/work/eri-support-docs/eri-support-docs/public'
copyright	NoneType	None
google_analytics	NoneType	None
dev_addr	_IpAddressValue	_IpAddressValue(host='127.0.0.1', port=8000)
use_directory_urls	bool	True
repo_url	str	'https://github.com/MattBixley/eri-support-docs'
repo_name	str	'GitHub'
edit_uri_template	NoneType	None
edit_uri	str	'edit/main/docs/'
extra_css	list	['assets/stylesheets/neoteroi-mkdocs.css', 'assets/stylesheets/footer.css', 'assets/stylesheets/custom_admonations.css', 'assets/stylesheets/theme.css']
extra_javascript	list	['assets/javascripts/general.js', 'https://status.nesi.org.nz/embed/script.js', 'js/open_in_new_tab.js']
extra_templates	list	[]
markdown_extensions	list	['toc', 'tables', 'fenced_code', 'admonition', 'pymdownx.details', 'pymdownx.superfences', 'pymdownx.highlight', 'pymdownx.inlinehilite', 'pymdownx.tabbed', 'pymdownx.snippets', 'attr_list', 'abbr', 'neoteroi.cards', 'neoteroi.timeline', 'footnotes']
mdx_configs	dict	toc [dict], pymdownx.tabbed [dict]
strict	bool	False
remote_branch	str	'gh-pages'
remote_name	str	'origin'
extra	LegacyConfig	{}
plugins	PluginCollection	material/search [SearchPlugin], open-in-new-tab [OpenInNewTabPlugin], redirects [RedirectPlugin], awesome-pages [AwesomePagesPlugin], material/tags [TagsPlugin], git-revision-date-localized [GitRevisionDateLocalizedPlugin], macros [MacrosPlugin], mkdocs_hooks.py [module]
hooks	dict	mkdocs_hooks.py [module]
watch	list	[]
validation	Validation	{'nav': {'omitted_files': 20, 'not_found': 30, 'absolute_links': 20}, 'links': {'not_found': 30, 'absolute_links': 20, 'unrecognized_links': 20, 'anchors': 20}}

Macros

These macros have been defined programmatically for this environment (module or pluglets).

Variable	Type	Content
context	function	(obj, var, value, e) Default mkdocs_macro List the defined variables
macros_info	function	() Test/debug function: list useful documentation on the mkdocs_macro environment.
now	function	() Get the current time (returns a datetime object). Used alone, it provides a timestamp. To get the year use now().year, for the month number now().month, etc.
fix_url	function	(url, r) If url is relative, fix it so that it points to the docs diretory. This is necessary because relative links in markdown must be adapted in html ('img/foo.png' => '../img/img.png').

Git Information

Information available on the last commit and the git repository containing the documentation project:

e.g. {{ git.message }}

Variable	Type	Content
status	bool	True
date	datetime	datetime.datetime(2024, 10, 17, 14, 53, 41, tzinfo=tzoffset(None, 46800))
short_commit	str	'2d39735'
commit	str	'2d39735fdcef5f37e1b3644d6bba5f4d5cb18ba1'
tag	str	''
short_tag	str	''
author	str	'Matt Bixley'
author_email	str	'mattbixley72@gmail.com'
committer	str	'GitHub'
committer_email	str	'noreply@github.com'
date_ISO	str	'Thu Oct 17 14:53:41 2024 +1300'
message	str	'Merge pull request #2 from MattBixley/resonant-panther\n\nResonant panther'
raw	str	'commit 2d39735fdcef5f37e1b3644d6bba5f4d5cb18ba1\nMerge: e537d18 d39c5bc\nAuthor: Matt Bixley \nDate: Thu Oct 17 14:53:41 2024 +1300\n\n Merge pull request #2 from MattBixley/resonant-panther\n \n Resonant panther'
root_dir	str	'/home/runner/work/eri-support-docs/eri-support-docs'

Page Attributes

Provided by MkDocs. These attributes change for every page (the attributes shown are for this page).

e.g. {{ page.title }}

See also the MkDocs documentation on the page object.

Variable	Type	Content
file	File	src_uri = 'MACROS.md', src_dir = '/home/runner/work/eri-support-docs/eri-support-docs/docs', dest_dir = '/home/runner/work/eri-support-docs/eri-support-docs/public', use_directory_urls = True, inclusion [InclusionLevel], name = 'MACROS', dest_uri = 'MACROS/index.html', page [Page], url = 'MACROS/', abs_src_path = '/home/runner/work/eri-support-docs/eri-support-docs/docs/MACROS.md'
children	NoneType	None
previous_page	Page	Page(title='GLOSSARY', url='/eri-support-docs/GLOSSARY/')
next_page	Page	Page(title=[blank], url='/eri-support-docs/NEWPAGE/')
_Page__active	bool	False
update_date	str	'2024-10-17'
canonical_url	str	'https://mattbixley.github.io/eri-support-docs/MACROS/'
abs_url	str	'/eri-support-docs/MACROS/'
edit_url	str	'https://github.com/MattBixley/eri-support-docs/edit/main/docs/MACROS.md'
markdown	str	'**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://https://mattbixley.github.io/eri-support-docs/MACROS/)**{ .hidden }\n\n## Info about macros\n\n{{ macros_info() }}\n'
_title_from_render	NoneType	None
content	NoneType	None
toc	list	[]
meta	dict	search [dict], git_revision_date_localized = 'October 17, 2024', git_revision_date_localized_raw_date = 'October 17, 2024', git_revision_date_localized_raw_datetime = 'October 17, 2024 01:15:53', git_revision_date_localized_raw_iso_date = '2024-10-17', git_revision_date_localized_raw_iso_datetime = '2024-10-17 01:15:53', git_revision_date_localized_raw_timeago = '', git_revision_date_localized_raw_custom = '17. October 2024', git_site_revision_date_localized = 'October 17, 2024', git_site_revision_date_localized_raw_date = 'October 17, 2024', git_site_revision_date_localized_raw_datetime = 'October 17, 2024 01:49:07', git_site_revision_date_localized_raw_iso_date = '2024-10-17', git_site_revision_date_localized_raw_iso_datetime = '2024-10-17 01:49:07', git_site_revision_date_localized_raw_timeago = '', git_site_revision_date_localized_raw_custom = '17. October 2024', git_creation_date_localized = 'November 16, 2023', git_creation_date_localized_raw_date = 'November 16, 2023', git_creation_date_localized_raw_datetime = 'November 16, 2023 02:16:32', git_creation_date_localized_raw_iso_date = '2023-11-16', git_creation_date_localized_raw_iso_datetime = '2023-11-16 02:16:32', git_creation_date_localized_raw_timeago = '', git_creation_date_localized_raw_custom = '16. November 2023'

To have all titles of all pages, use:

{% for page in navigation.pages %}
- {{ page.title }}
{% endfor %}

Plugin Filters

These filters are provided as a standard by the macros plugin.

Variable	Type	Content
pretty	function	(var_list, var, var_type, content, rows, header, e) Default mkdocs_macro Prettify a dictionary or object (used for environment documentation, or debugging).

Builtin Jinja2 Filters

These filters are provided by Jinja2 as a standard.

See also the Jinja2 documentation on builtin filters).

Variable	Type	Content
abs	builtin_function_or_method	Return the absolute value of the argument.
attr	function	(environment, obj, name, value) Get an attribute of an object. foo|attr("bar") works like foo.bar just that always an attribute is returned and items are not looked up.
batch	function	(value, linecount, fill_with, tmp, item) A filter that batches items. It works pretty much like slice just the other way round. It returns a list of lists with the given number of items. If you provide a second parameter this is used to fill up missing items. See this example.
capitalize	function	(s) Capitalize a value. The first character will be uppercase, all others lowercase.
center	function	(value, width) Centers the value in a field of a given width.
count	builtin_function_or_method	Return the number of items in a container.
d	function	(value, default_value, boolean) If the value is undefined it will return the passed default value, otherwise the value of the variable.
default	function	(value, default_value, boolean) If the value is undefined it will return the passed default value, otherwise the value of the variable.
dictsort	function	(value, case_sensitive, by, reverse, sort_func) Sort a dict and yield (key, value) pairs. Python dicts may not be in the order you want to display them in, so sort them first.
e	builtin_function_or_method	Replace the characters &, <, >, ', and " in the string with HTML-safe sequences. Use this if you need to display text that might contain such characters in HTML.
escape	builtin_function_or_method	Replace the characters &, <, >, ', and " in the string with HTML-safe sequences. Use this if you need to display text that might contain such characters in HTML.
filesizeformat	function	(value, binary, bytes, base, prefixes, i, prefix, unit) Format the value like a 'human-readable' file size (i.e. 13 kB, 4.1 MB, 102 Bytes, etc). Per default decimal prefixes are used (Mega, Giga, etc.), if the second parameter is set to True the binary prefixes are used (Mebi, Gibi).
first	function	(args, kwargs, b) Return the first item of a sequence.
float	function	(value, default) Convert the value into a floating point number. If the conversion doesn't work it will return 0.0. You can override this default using the first parameter.
forceescape	function	(value) Enforce HTML escaping. This will probably double escape variables.
format	function	(value, args, kwargs) Apply the given values to a printf-style_ format string, like string % values.
groupby	function	(args, kwargs, b) Group a sequence of objects by an attribute using Python's :func:itertools.groupby. The attribute can use dot notation for nested access, like "address.city". Unlike Python's groupby, the values are sorted first so only one group is returned for each unique value.
indent	function	(s, width, first, blank, newline, rv, lines) Return a copy of the string with each line indented by 4 spaces. The first line and blank lines are not indented by default.
int	function	(value, default, base) Convert the value into an integer. If the conversion doesn't work it will return 0. You can override this default using the first parameter. You can also override the default base (10) in the second parameter, which handles input with prefixes such as 0b, 0o and 0x for bases 2, 8 and 16 respectively. The base is ignored for decimal numbers and non-string values.
join	function	(args, kwargs, b) Return a string which is the concatenation of the strings in the sequence. The separator between elements is an empty string per default, you can define it with the optional parameter.
last	function	(environment, seq) Return the last item of a sequence.
length	builtin_function_or_method	Return the number of items in a container.
list	function	(args, kwargs, b) Convert the value into a list. If it was a string the returned list will be a list of characters.
lower	function	(s) Convert a value to lowercase.
items	function	(value) Return an iterator over the (key, value) items of a mapping.
map	function	(args, kwargs, b) Applies a filter on a sequence of objects or looks up an attribute. This is useful when dealing with lists of objects but you are really only interested in a certain value of it.
min	function	(environment, value, case_sensitive, attribute) Return the smallest item from the sequence.
max	function	(environment, value, case_sensitive, attribute) Return the largest item from the sequence.
pprint	function	(value) Pretty print a variable. Useful for debugging.
random	function	(context, seq) Return a random item from the sequence.
reject	function	(args, kwargs, b) Filters a sequence of objects by applying a test to each object, and rejecting the objects with the test succeeding.
rejectattr	function	(args, kwargs, b) Filters a sequence of objects by applying a test to the specified attribute of each object, and rejecting the objects with the test succeeding.
replace	function	(eval_ctx, s, old, new, count) Return a copy of the value with all occurrences of a substring replaced with a new one. The first argument is the substring that should be replaced, the second is the replacement string. If the optional third argument count is given, only the first count occurrences are replaced.
reverse	function	(value, rv, e) Reverse the object or return an iterator that iterates over it the other way round.
round	function	(value, precision, method, func) Round the number to a given precision. The first parameter specifies the precision (default is 0), the second the rounding method.
safe	function	(value) Mark the value as safe which means that in an environment with automatic escaping enabled this variable will not be escaped.
select	function	(args, kwargs, b) Filters a sequence of objects by applying a test to each object, and only selecting the objects with the test succeeding.
selectattr	function	(args, kwargs, b) Filters a sequence of objects by applying a test to the specified attribute of each object, and only selecting the objects with the test succeeding.
slice	function	(args, kwargs, b) Slice an iterator and return a list of lists containing those items. Useful if you want to create a div containing three ul tags that represent columns.
sort	function	(environment, value, reverse, case_sensitive, attribute, key_func) Sort an iterable using Python's :func:sorted.
string	builtin_function_or_method	Convert an object to a string if it isn't already. This preserves a :class:Markup string rather than converting it back to a basic string, so it will still be marked as safe and won't be escaped again.
striptags	function	(value) Strip SGML/XML tags and replace adjacent whitespace by one space.
sum	function	(args, kwargs, b) Returns the sum of a sequence of numbers plus the value of parameter 'start' (which defaults to 0). When the sequence is empty it returns start.
title	function	(s, item) Return a titlecased version of the value. I.e. words will start with uppercase letters, all remaining characters are lowercase.
trim	function	(value, chars) Strip leading and trailing characters, by default whitespace.
truncate	function	(env, s, length, killwords, end, leeway, result) Return a truncated copy of the string. The length is specified with the first parameter which defaults to 255. If the second parameter is true the filter will cut the text at length. Otherwise it will discard the last word. If the text was in fact truncated it will append an ellipsis sign ("..."). If you want a different ellipsis sign than "..." you can specify it using the third parameter. Strings that only exceed the length by the tolerance margin given in the fourth parameter will not be truncated.
unique	function	(environment, value, case_sensitive, attribute, getter, seen, item, key) Returns a list of unique items from the given iterable.
upper	function	(s) Convert a value to uppercase.
urlencode	function	(value, items) Quote data for use in a URL path or query using UTF-8.
urlize	function	(eval_ctx, value, trim_url_limit, nofollow, target, rel, extra_schemes, policies, rel_parts, scheme, rv) Convert URLs in text into clickable links.
wordcount	function	(s) Count the words in that string.
wordwrap	function	(environment, s, width, break_long_words, wrapstring, break_on_hyphens, textwrap, line) Wrap a string to the given width. Existing newlines are treated as paragraphs to be wrapped separately.
xmlattr	function	(eval_ctx, d, autospace, items, key, value, rv) Create an SGML/XML attribute string based on the items in a dict.
tojson	function	(eval_ctx, value, indent, policies, dumps, kwargs) Serialize an object to a string of JSON, and mark it safe to render in HTML. This filter is only for use in HTML documents.