MACROS
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Info about macros¶
Macros Plugin Environment¶
General List¶
All available variables and filters within the macros plugin:
| Variable | Type | Content |
|---|---|---|
| extra | dict | slurm = 'slurm-25.05.6', project_code = 'nesi99991', working_directory = ['/nesi/nobackup/nesi99991', 'introhpc2610'], example_script = 'sum_matrix.r', exercise = 'https://docs.google.com/spreadsheets/d/1D5PnhE6iJOB3ZKkDCiBHnk5CNZlhmj_gS-IXKGkkVoI/edit?usp=sharing', status = ['deprecated', 'new', 'tutorial'], analytics [dict], globus_collection_storage = 'REANNZ Mahuika', globus_collection_freezer = 'REANNZ Freezer', globus_collection_rdc = 'REANNZ Research Developer Cloud (RDC)', globus_collection_endpoint = 'REANNZ Data Transfer Node Tamaki', intermediate_hpc_job_id_01 = 9296168, intermediate_hpc_job_id_02 = 9310633, intermediate_hpc_job_id_03a = 9308257, intermediate_hpc_job_id_03b = 9308287, intermediate_hpc_job_id_03c = 9308288 |
| config | MkDocsConfig | {'config_file_path': '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/mkdocs.yml', 'site_name': 'Support Documentation', 'nav': None, 'pages': None, 'exclude_docs': None, 'draft_docs': None, 'not_in_nav': GitIgnoreSpec(patterns=[GitIgnoreSpecPattern(pattern='/*.md', include=True), GitIgnoreSpecPattern(pattern='/assets/', include=True)], backend='best'), 'site_url': 'https://docs.nesi.org.nz/', 'site_description': 'Support Documentation', 'site_author': None, 'theme': Theme(name='material', dirs=['/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/overrides', '/home/runner/.local/lib/python3.12/site-packages/material/templates', '/home/runner/.local/lib/python3.12/site-packages/mkdocs/templates'], static_templates={'404.html', 'sitemap.xml'}, name='material', locale=Locale('en'), language='en', direction=None, features=['announce.dismiss', 'navigation.indexes', 'navigation.instant', 'navigation.instant.progress', '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_reannz.ico', logo='assets/icons/logo_reannz.svg', palette=[{'media': '(prefers-color-scheme)', 'toggle': {'icon': 'material/brightness-auto', 'name': 'Switch to light mode'}}, {'media': '(prefers-color-scheme: light)', 'scheme': 'default', 'toggle': {'icon': 'material/lightbulb', 'name': 'Switch to dark mode'}, 'primary': 'custom'}, {'media': '(prefers-color-scheme: dark)', 'scheme': 'slate', 'primary': 'custom', 'accent': 'custom', 'toggle': {'icon': 'material/lightbulb-outline', 'name': 'Switch to light mode'}}]), 'docs_dir': '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/docs', 'site_dir': '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/public/nesi/support-docs/numa-domains', 'copyright': None, 'google_analytics': None, 'dev_addr': _IpAddressValue(host='127.0.0.1', port=8000), 'use_directory_urls': True, 'repo_url': 'https://github.com/nesi/support-docs', 'repo_name': 'GitHub', 'edit_uri_template': None, 'edit_uri': 'edit/main/docs/', 'extra_css': ['assets/stylesheets/theme.css', 'assets/stylesheets/chat.css'], 'extra_javascript': ['https://cdnjs.cloudflare.com/ajax/libs/ical.js/1.3.0/ical.min.js', 'https://status.nesi.org.nz/embed/script.js', 'assets/javascripts/mathjax.js', 'https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js', 'assets/javascripts/general.js', 'assets/javascripts/chat.js', 'assets/javascripts/supportedApplications.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.magiclink', 'pymdownx.tabbed', 'pymdownx.snippets', 'attr_list', 'abbr', 'footnotes', 'def_list', 'pymdownx.arithmatex'], 'mdx_configs': {'toc': {'baselevel': 1, 'permalink': True, 'toc_depth': 3, 'title': 'On this page'}, 'pymdownx.superfences': {'custom_fences': [{'name': 'mermaid', 'class': 'mermaid', 'format': |
| environment | dict | system = 'Linux', system_version = '7.0.0-1017-azure', python_version = '3.12.3', mkdocs_version = '1.6.1', macros_plugin_version = '1.5.0', jinja2_version = '3.1.6' |
| plugin | LegacyConfig | {'module_name': 'macro_hooks', 'modules': [], 'render_by_default': True, 'force_render_paths': '', 'include_dir': 'overrides', 'include_yaml': [], 'j2_block_start_string': '', 'j2_block_end_string': '', 'j2_variable_start_string': '', 'j2_variable_end_string': '', 'j2_comment_start_string': '', 'j2_comment_end_string': '', 'j2_extensions': [], 'on_undefined': 'keep', 'on_error_fail': False, 'verbose': True} |
| git | dict | status = True, date [datetime], short_commit = 'cd8a5744', commit = 'cd8a574416b8e4d5edf33e992d45491f7ea14f9b', tag = '', short_tag = '', author = 'geoffreyweal', author_email = 'geoffrey.weal@gmail.com', committer = 'geoffreyweal', committer_email = 'geoffrey.weal@gmail.com', date_ISO = 'Wed Nov 4 13:52:24 2026 +1300', message = "Add NUMA Domains page\n\nAdd a page that explains NUMA domains for researchers who are new to\ncomputers: cores and memory, near and far memory (told as a story about\nlabs and fridges), how Mahuika's nodes are split into NUMA domains, why\nit matters more on Mahuika than on a desktop, when it slows a job down,\nhow to check a job's NUMA domains, how to keep work near its data, and\nhow Slurm treats each NUMA domain as a socket.\n\nAdd five diagrams for the page, and link to it from Thread Placement and\nThread Affinity, Hardware, and VASP. Correct the VASP sentence that said\nNUMA domains contain the L3 cache, and fix the --extra-node-into typo on\nthe Thread Placement page.\n\nCo-Authored-By: Claude Opus 5.5 |
| slurm | str | 'slurm-25.05.6' |
| project_code | str | 'nesi99991' |
| working_directory | SuperList | ['/nesi/nobackup/nesi99991', 'introhpc2610'] |
| example_script | str | 'sum_matrix.r' |
| exercise | str | 'https://docs.google.com/spreadsheets/d/1D5PnhE6iJOB3ZKkDCiBHnk5CNZlhmj_gS-IXKGkkVoI/edit?usp=sharing' |
| status | SuperList | ['deprecated', 'new', 'tutorial'] |
| analytics | SuperDict | provider = 'google', property = 'G-TVQR4R1F40' |
| globus_collection_storage | str | 'REANNZ Mahuika' |
| globus_collection_freezer | str | 'REANNZ Freezer' |
| globus_collection_rdc | str | 'REANNZ Research Developer Cloud (RDC)' |
| globus_collection_endpoint | str | 'REANNZ Data Transfer Node Tamaki' |
| intermediate_hpc_job_id_01 | int | 9296168 |
| intermediate_hpc_job_id_02 | int | 9310633 |
| intermediate_hpc_job_id_03a | int | 9308257 |
| intermediate_hpc_job_id_03b | int | 9308287 |
| intermediate_hpc_job_id_03c | int | 9308288 |
| applications | CaseInsensitiveDict | ABAQUS [dict], ABRicate [dict], abritamr [dict], Abseil [dict], ABySS [dict], ACTC [dict], AdapterRemoval [dict], AdaptiveCpp [dict], Advisor [dict], AGAT [dict], AGE [dict], AlphaFold [dict], AlphaFold2DB [dict], AlphaFold3DB [dict], AlwaysIntelMKL [dict], Amber [dict], AMOS [dict], AMRFinderPlus [dict], Anaconda3 [dict], angsd [dict], ANIcalculator [dict], ANNOVAR [dict], ANSYS [dict], ant [dict], antiSMASH [dict], ANTs [dict], any2fasta [dict], AOCC [dict], AOCL-BLAS [dict], AOCL-BLIS [dict], AOCL-FFTW [dict], AOCL-ScaLAPACK [dict], Apptainer [dict], APR [dict], APR-util [dict], ARAGORN [dict], argtable [dict], aria2 [dict], ARIBA [dict], Armadillo [dict], arpack-ng [dict], Arrow [dict], ASAGI [dict], Aspera-CLI [dict], at-spi2-atk [dict], at-spi2-core [dict], ATK [dict], attr [dict], AUGUSTUS [dict], Autocycler [dict], AutoDock-GPU [dict], AutoDock_Vina [dict], Avogadro2 [dict], awscli [dict], azul-zulu [dict], bakta [dict], BamTools [dict], bamUtil [dict], Bandage [dict], barrnap [dict], Basilisk [dict], BayesAss [dict], BayeScan [dict], BayPass [dict], BBMap [dict], BCFtools [dict], BCL-Convert [dict], bcl2fastq2 [dict], Beagle [dict], beagle-lib [dict], BEAST [dict], BEDOPS [dict], BEDTools [dict], BEEF [dict], best [dict], BGC-Bayesian-genomic-clines [dict], Bifrost [dict], BiG-SCAPE [dict], binutils [dict], Bio-DB-BigFile [dict], Bio-DB-HTS [dict], bioawk [dict], BioPP [dict], Bismark [dict], Bison [dict], bitsandbytes [dict], BLAST [dict], BLASTDB [dict], BLAT [dict], BLIS [dict], BOLT-LMM [dict], Boost [dict], Boost.Python-NumPy [dict], boto3 [dict], Bowtie [dict], Bowtie2 [dict], Bracken [dict], BRAKER [dict], breseq [dict], buildenv [dict], BUSCO [dict], BWA [dict], bwa-mem2 [dict], bzip2 [dict], c-ares [dict], cairo [dict], Canu [dict], CapnProto [dict], Catch2 [dict], CD-HIT [dict], cdbfasta [dict], CDO [dict], CellRanger [dict], Centrifuge [dict], Cereal [dict], CFITSIO [dict], CGAL [dict], chainforge [dict], Check [dict], CheckM [dict], CheckM2 [dict], CheckV [dict], chewBBACA [dict], chopper [dict], cimfomfa [dict], Circlator [dict], Circos [dict], Clair3 [dict], Clang [dict], Clustal-Omega [dict], ClustalW2 [dict], CMake [dict], CMFGEN [dict], CNVnator [dict], CNVpytor [dict], code-server [dict], compleasm [dict], COMSOL [dict], CONCOCT [dict], CoordgenLibs [dict], CoverM [dict], CP2K [dict], CPMD [dict], CppUnit [dict], CRABS [dict], CRAMINO [dict], CREST [dict], cromwell [dict], csvtk [dict], ctags [dict], ctffind [dict], CubeLib [dict], CubeWriter [dict], CUDA [dict], cuDNN [dict], cURL [dict], cutadapt [dict], cuteSV [dict], Cytoscape [dict], cyvcf2 [dict], D-Genies [dict], dadi [dict], DAS_Tool [dict], datasets [dict], DB [dict], DB_File [dict], DBCSR [dict], DBD-mysql [dict], DBus [dict], DeconSeq [dict], DeepLabCut [dict], DeePMD-kit [dict], DeePMD-plugin [dict], deepTools [dict], Delft3D [dict], Delft3D_FM [dict], Delly [dict], devtools [dict], DFT-D4 [dict], DIAMOND [dict], Dorado [dict], dorado [dict], double-conversion [dict], Doxygen [dict], DRAM [dict], drep [dict], Dsuite [dict], dtcmp [dict], duphold [dict], duplex-tools [dict], easi [dict], EasyBuild [dict], ecCodes [dict], edlib [dict], eDNA [dict], EDTA [dict], EESSI [dict], eggnog-mapper [dict], Eigen [dict], EIGENSOFT [dict], ELPA [dict], EMAN2 [dict], EMBOSS [dict], Embree [dict], emmtyper [dict], Emu [dict], ensmallen [dict], entrez-direct [dict], ESMF [dict], ETE [dict], EukRep-EukCC [dict], ExaBayes [dict], ExaML [dict], Exonerate [dict], exonerate [dict], ExpansionHunter [dict], expat [dict], f90wrap [dict], Faiss [dict], FastANI [dict], FastME [dict], fastp [dict], FastQ_Screen [dict], FastQC [dict], Fastsimcoal2 [dict], fastStructure [dict], FastTree [dict], FASTX-Toolkit [dict], FCM [dict], FDS [dict], FEBio [dict], FFmpeg [dict], FFTW [dict], FFTW.MPI [dict], fgbio [dict], FIGARO [dict], File-Rename [dict], FileSender [dict], Filtlong [dict], FimTyper [dict], fineRADstructure [dict], fineSTRUCTURE [dict], flatbuffers [dict], flex [dict], FlexiBLAS [dict], FLTK [dict], Flye [dict], fmt [dict], Foldseek [dict], fontconfig [dict], foss [dict], FragGeneScan [dict], FreeBayes [dict], FreeFEM [dict], FreeSurfer [dict], freetype [dict], FreeXL [dict], FriBidi [dict], funcx-endpoint [dict], g2clib [dict], GATK [dict], Gaussian [dict], GCC [dict], GCCcore [dict], gcloud [dict], GD [dict], GDAL [dict], Gdk-Pixbuf [dict], GEMMA [dict], gemmforge [dict], GeneMark-ES [dict], GeneMark-ET [dict], GenomeThreader [dict], genometools [dict], GenoVi [dict], GEOS [dict], GetOrganelle [dict], gettext [dict], gfastats [dict], gfatools [dict], gfbf [dict], gffread [dict], giflib [dict], gimkl [dict], gimpi [dict], git [dict], GLib [dict], GlimmerHMM [dict], Globus-CLI [dict], globus-compute-endpoint [dict], GLPK [dict], GMAP-GSNAP [dict], GMP [dict], gmsh [dict], GMT [dict], gnuplot [dict], Go [dict], GOLD [dict], gompi [dict], google-sparsehash [dict], googletest [dict], GPAW [dict], gperf [dict], GPUMD [dict], Graphviz [dict], GRASS [dict], GRIDSS [dict], GROMACS [dict], GROMACS_CP2K [dict], GSL [dict], GST-plugins-base [dict], GStreamer [dict], GTDB-Tk [dict], GTK+ [dict], GTS [dict], Gubbins [dict], GUSHR [dict], h5pp [dict], h5py [dict], HAL [dict], haplocheck [dict], HarfBuzz [dict], HDF [dict], HDF5 [dict], HH-suite [dict], hifiasm [dict], HISAT2 [dict], HMMER [dict], HMMER2 [dict], HpcGridRunner [dict], HTSeq [dict], HTSlib [dict], Humann [dict], hwloc [dict], HybPiper [dict], Hydra [dict], Hypre [dict], iccifort [dict], ICU [dict], IDBA-UD [dict], ifbf [dict], igraph [dict], IGV [dict], iimpi [dict], ImageMagick [dict], imkl [dict], imkl-FFTW [dict], impalajit [dict], impi [dict], Infernal [dict], intel [dict], intel-compilers [dict], InterProScan [dict], iofbf [dict], iompi [dict], ipyrad [dict], IQ-TREE [dict], IRkernel [dict], ISA-L [dict], JAGS [dict], JasPer [dict], Java [dict], jbigkit [dict], jcvi [dict], Jellyfish [dict], jemalloc [dict], json-c [dict], json-fortran [dict], JsonCpp [dict], Julia [dict], JupyterLab [dict], jvarkit [dict], Kaiju [dict], Kalign [dict], kalign2 [dict], kallisto [dict], KAT [dict], KEALib [dict], Kent-core [dict], Kent_tools [dict], kineto [dict], kma [dict], KMC [dict], KmerGenie [dict], KorfSNAP [dict], Kraken2 [dict], KronaTools [dict], LAME [dict], LAMMPS [dict], LAST [dict], LASTZ [dict], LDC [dict], LEfSe [dict], LegacySystemLibs [dict], leidenalg [dict], levmar [dict], libaec [dict], libarchive [dict], libcircle [dict], libcuda-stub [dict], libdeepmd [dict], libdeflate [dict], libdrm [dict], libdwarf [dict], libepoxy [dict], libevent [dict], libffi [dict], libFLAME [dict], libgcrypt [dict], libgd [dict], libgeotiff [dict], libgit2 [dict], libGLU [dict], libglvnd [dict], libgpg-error [dict], libgpuarray [dict], libgtextutils [dict], libiconv [dict], Libint [dict], libjpeg-turbo [dict], libKML [dict], libleidenalg [dict], libpciaccess [dict], libpmi [dict], libpng [dict], libreadline [dict], libRmath [dict], libsodium [dict], libspatialite [dict], libStatGen [dict], LIBSVM [dict], LibTIFF [dict], libtool [dict], libunwind [dict], libvdwxc [dict], libvori [dict], libxc [dict], libxml2 [dict], libxs [dict], libxslt [dict], libxsmm [dict], libzstd [dict], Liftoff [dict], lighttpd [dict], likwid [dict], LINKS [dict], LISFLOOD-FP [dict], LittleCMS [dict], LLVM [dict], LMDB [dict], LongStitch [dict], lp_solve [dict], LSD2 [dict], LTR_retriever [dict], LUMPY [dict], lwgrp [dict], lz4 [dict], LZO [dict], M4 [dict], maeparser [dict], maf_stream [dict], MAFFT [dict], magma [dict], MAKER [dict], Mamba [dict], manta [dict], mapDamage [dict], Marimo [dict], Mash [dict], MashMap [dict], Mashtree [dict], MaSuRCA [dict], MATLAB [dict], matlab-proxy [dict], Maven [dict], MaxBin [dict], MCL [dict], MCR [dict], mctc-lib [dict], MDI [dict], medaka [dict], MEGAHIT [dict], megalodon [dict], Merqury [dict], Mesa [dict], Meson [dict], MetaBAT [dict], METABOLIC [dict], MetaEuk [dict], MetaGeneAnnotator [dict], MetalWalls [dict], MetaPhlAn [dict], MetaPhlAn2 [dict], MetaSV [dict], metaWRAP [dict], Metaxa2 [dict], METIS [dict], micro [dict], MiMiC [dict], MiMiC-CommLib [dict], miniasm [dict], miniBUSCO [dict], Miniconda3 [dict], Miniforge3 [dict], minigraph [dict], Minimac3 [dict], Minimac4 [dict], minimap2 [dict], miniprot [dict], MiniZinc [dict], miRDeep2 [dict], MitoZ [dict], Mmg [dict], MMseqs2 [dict], modbam2bed [dict], ModDotPlot [dict], ModelTest-NG [dict], modkit [dict], Molpro [dict], Mono [dict], Monocle3 [dict], mosdepth [dict], Mothur [dict], mpcci [dict], MPFR [dict], MrBayes [dict], MultiQC [dict], MUMmer [dict], MUMPS [dict], muParser [dict], MUSCLE [dict], NAMD [dict], nano [dict], NanoComp [dict], nanofilt [dict], nanoget [dict], NanoLyse [dict], nanomath [dict], NanoPlot [dict], nanopolish [dict], nanoQC [dict], NanoStat [dict], NASM [dict], ncbi-vdb [dict], NCCL [dict], NCL [dict], NCO [dict], ncurses [dict], ncview [dict], ne [dict], NECAT [dict], NeSI [dict], nesi_eb [dict], netCDF [dict], netCDF-C++ [dict], netCDF-C++4 [dict], netCDF-Fortran [dict], NewHybrids [dict], Newton-X [dict], Nextflow [dict], NextPolish2 [dict], nf-core [dict], NGS [dict], Nim [dict], Ninja [dict], NLopt [dict], nodejs [dict], NONMEM [dict], nseg [dict], Nsight-Compute [dict], Nsight-Systems [dict], NSPR [dict], NSS [dict], nsync [dict], nullarbor [dict], numactl [dict], NVHPC [dict], nvidia-compilers [dict], nvofbf [dict], nvompi [dict], NWChem [dict], OBITools [dict], ollama [dict], ont-guppy-gpu [dict], OPARI2 [dict], OpenBabel [dict], OpenBLAS [dict], OpenCV [dict], OpenFOAM [dict], OpenFold3 [dict], OpenJPEG [dict], OpenMC [dict], OpenMPI [dict], OpenSees [dict], OpenSeesPy [dict], OpenSlide [dict], OpenSSL [dict], ORCA [dict], OrthoFinder [dict], OSPRay [dict], OSU-Micro-Benchmarks [dict], OTF2 [dict], padloc [dict], pairtools [dict], PALEOMIX [dict], PAML [dict], panaroo [dict], pandoc [dict], Pango [dict], PAPI [dict], Parallel [dict], parallel-fastq-dump [dict], ParallelIO [dict], ParaView [dict], ParMETIS [dict], patchelf [dict], pauvre [dict], PCRE [dict], PCRE2 [dict], PDAL [dict], PEAR [dict], Perl [dict], PETSc [dict], pggb [dict], pgge [dict], PGPLOT [dict], phonopy [dict], PhyloPhlAn [dict], PhyML [dict], phyx [dict], picard [dict], pigz [dict], PILERCR [dict], Pilon [dict], PISM [dict], pixi [dict], pixman [dict], PlasMAAG [dict], PLINK [dict], PLUMED [dict], Pluto [dict], PnetCDF [dict], pod5 [dict], Porechop [dict], Porechop_ABI [dict], PostgreSQL [dict], pplacer [dict], PRANK [dict], preseq [dict], prodigal [dict], Prodigal [dict], prodigal-gv [dict], PROJ [dict], prokka [dict], Proteinortho [dict], ProtHint [dict], protobuf [dict], psmc [dict], PSpaMM [dict], pstoedit [dict], pullseq [dict], PUMI [dict], purge_dups [dict], purge_haplotigs [dict], pv [dict], pyani [dict], pybind11 [dict], pycoQC [dict], pymol-open-source [dict], PyQt [dict], Python [dict], Python-Geo [dict], python-igraph [dict], PyTorch [dict], PyTorch-Lightning [dict], qcat [dict], QChem [dict], QIIME2 [dict], Qt5 [dict], QuantumESPRESSO [dict], QUAST [dict], QuickTree [dict], R [dict], R-bundle-Bioconductor [dict], R-Geo [dict], R-JAGS [dict], Racon [dict], Ragout [dict], randfold [dict], RapidNJ [dict], rasusa [dict], Ratatosk [dict], Raven [dict], RAxML [dict], RAxML-NG [dict], rclone [dict], Rcorrector [dict], RDKit [dict], RDP-Classifier [dict], RE2 [dict], re2c [dict], RECON [dict], Relion [dict], RepeatMasker [dict], RepeatModeler [dict], RepeatScout [dict], REViewer [dict], RFdiffusion [dict], RFPlasmid [dict], Riskscape [dict], RJMCMC [dict], RMBlast [dict], RNAmmer [dict], rnaQUAST [dict], Roary [dict], ROOT [dict], Rosetta [dict], RSEM [dict], RSGISLib [dict], RStudio-Server [dict], Ruby [dict], Rust [dict], s3cmd [dict], safestringlib [dict], SAGE [dict], Salmon [dict], Sambamba [dict], samblaster [dict], samclip [dict], SAMtools [dict], sbt [dict], sc-RNA [dict], ScaLAPACK [dict], SCOTCH [dict], screen_assembly [dict], SDL2 [dict], SeisSol [dict], SEPP [dict], SeqAn [dict], SeqAn3 [dict], SeqKit [dict], seqmagick [dict], seqtk [dict], SHAPEIT4 [dict], shrinkwrap [dict], SiBELia [dict], Siesta [dict], SignalP [dict], simuG [dict], SIONlib [dict], SIP [dict], sismonr [dict], SKA2 [dict], skani [dict], SKESA [dict], SLEPc [dict], slow5-dorado [dict], slow5tools [dict], smoove [dict], SMRT-Link [dict], snakemake [dict], snappy [dict], Sniffles [dict], snippy [dict], snp-sites [dict], snpEff [dict], SNVoter-NanoMethPhase [dict], somalier [dict], SortMeRNA [dict], SourceTracker [dict], SPAdes [dict], spaln [dict], Spark [dict], spdlog [dict], SpectrA [dict], spoa [dict], SQLite [dict], squashfs-tools [dict], SqueezeMeta [dict], sratoolkit [dict], SSAHA2 [dict], Stacks [dict], STAR [dict], StringTie [dict], Structure [dict], Subread [dict], Subversion [dict], SuiteSparse [dict], SUNDIALS [dict], SuperLU [dict], Supernova [dict], SURVIVOR [dict], swarm [dict], SWIG [dict], Szip [dict], tabix [dict], tabixpp [dict], tbb [dict], tbl2asn [dict], Tcl [dict], TCLAP [dict], tensorboardX [dict], TensorFlow [dict], TensorRT [dict], TEtranscripts [dict], Tk [dict], TMHMM [dict], tmux [dict], TOGA [dict], tomo [dict], TransDecoder [dict], TreeMix [dict], trf [dict], trimAl [dict], TrimGalore [dict], Trimmomatic [dict], Trinity [dict], Trinotate [dict], tRNAscan-SE [dict], Trycycler [dict], TSEBRA [dict], TUFLOW [dict], TuiView [dict], TURBOMOLE [dict], TurboVNC [dict], TWL-NINJA [dict], UCC [dict], UCC-CUDA [dict], UCX [dict], UCX-CUDA [dict], UDUNITS [dict], Unicycler [dict], unimap [dict], unrar [dict], USEARCH [dict], util-linux [dict], uv [dict], Valgrind [dict], VarScan [dict], VASP [dict], VBZ-Compression [dict], VCF-kit [dict], vcflib [dict], VCFtools [dict], vclust [dict], Velvet [dict], VelvetOptimiser [dict], VEP [dict], verkko [dict], vg [dict], VIBRANT [dict], ViennaRNA [dict], Vim [dict], VirHostMatcher [dict], VirSorter [dict], VMD [dict], Voro++ [dict], VSEARCH [dict], vt [dict], VTune [dict], Vulkan [dict], WAAFLE [dict], wannier90 [dict], WFA2 [dict], wgsim [dict], WhatsHap [dict], wheel [dict], Winnowmap [dict], Wise2 [dict], wtdbg [dict], wxWidgets [dict], x264 [dict], x265 [dict], Xerces-C++ [dict], xkbcommon [dict], xPore [dict], xtb [dict], XZ [dict], yacrd [dict], yajl [dict], yak [dict], yaml-cpp [dict], YAXT [dict], Z3 [dict], zellij [dict], ZeroMQ [dict], Zip [dict], zlib [dict], zstd [dict] |
| slurm_limits | dict | debug [dict], per_job [dict], per_user [dict], priority [dict] |
| macros | SuperDict | context [function], macros_info [function], now [function], fix_url [function], pages_with_tag [function] |
| filters | dict | pretty [function], relative_url [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 [function], escape [function], 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 [function], 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='/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/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/mkdocs.yml' |
| site_name | str | 'Support Documentation' |
| nav | NoneType | None |
| pages | NoneType | None |
| exclude_docs | NoneType | None |
| draft_docs | NoneType | None |
| not_in_nav | GitIgnoreSpec | GitIgnoreSpec(patterns=[GitIgnoreSpecPattern(pattern='/*.md', include=True), GitIgnoreSpecPattern(pattern='/assets/', include=True)], backend='best') |
| site_url | str | 'https://docs.nesi.org.nz/' |
| site_description | str | 'Support Documentation' |
| site_author | NoneType | None |
| theme | Theme | Theme(name='material', dirs=['/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/overrides', '/home/runner/.local/lib/python3.12/site-packages/material/templates', '/home/runner/.local/lib/python3.12/site-packages/mkdocs/templates'], static_templates={'404.html', 'sitemap.xml'}, name='material', locale=Locale('en'), language='en', direction=None, features=['announce.dismiss', 'navigation.indexes', 'navigation.instant', 'navigation.instant.progress', '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_reannz.ico', logo='assets/icons/logo_reannz.svg', palette=[{'media': '(prefers-color-scheme)', 'toggle': {'icon': 'material/brightness-auto', 'name': 'Switch to light mode'}}, {'media': '(prefers-color-scheme: light)', 'scheme': 'default', 'toggle': {'icon': 'material/lightbulb', 'name': 'Switch to dark mode'}, 'primary': 'custom'}, {'media': '(prefers-color-scheme: dark)', 'scheme': 'slate', 'primary': 'custom', 'accent': 'custom', 'toggle': {'icon': 'material/lightbulb-outline', 'name': 'Switch to light mode'}}]) |
| docs_dir | str | '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/docs' |
| site_dir | str | '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/public/nesi/support-docs/numa-domains' |
| 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/nesi/support-docs' |
| repo_name | str | 'GitHub' |
| edit_uri_template | NoneType | None |
| edit_uri | str | 'edit/main/docs/' |
| extra_css | list | ['assets/stylesheets/theme.css', 'assets/stylesheets/chat.css'] |
| extra_javascript | list | ['https://cdnjs.cloudflare.com/ajax/libs/ical.js/1.3.0/ical.min.js', 'https://status.nesi.org.nz/embed/script.js', 'assets/javascripts/mathjax.js', 'https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js', 'assets/javascripts/general.js', 'assets/javascripts/chat.js', 'assets/javascripts/supportedApplications.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.magiclink', 'pymdownx.tabbed', 'pymdownx.snippets', 'attr_list', 'abbr', 'footnotes', 'def_list', 'pymdownx.arithmatex'] |
| mdx_configs | dict | toc [dict], pymdownx.superfences [dict], pymdownx.tabbed [dict], pymdownx.arithmatex [dict] |
| strict | bool | False |
| remote_branch | str | 'gh-pages' |
| remote_name | str | 'origin' |
| extra | LegacyConfig | {'slurm': 'slurm-26.05.5', 'project_code': 'nesi99991', 'working_directory': ['/nesi/nobackup/nesi99991', 'introhpc2610'], 'example_script': 'sum_matrix.r', 'exercise': 'https://docs.google.com/spreadsheets/d/1D5PnhE6iJOB3ZKkDCiBHnk5CNZlhmj_gS-IXKGkkVoI/edit?usp=sharing', 'status': ['deprecated', 'new', 'tutorial'], 'analytics': {'provider': 'google', 'property': 'G-TVQR4R1F40'}, 'globus_collection_storage': 'REANNZ Mahuika', 'globus_collection_freezer': 'REANNZ Freezer', 'globus_collection_rdc': 'REANNZ Research Developer Cloud (RDC)', 'globus_collection_endpoint': 'REANNZ Data Transfer Node Tamaki', 'intermediate_hpc_job_id_01': 9296168, 'intermediate_hpc_job_id_02': 9310633, 'intermediate_hpc_job_id_03a': 9308257, 'intermediate_hpc_job_id_03b': 9308287, 'intermediate_hpc_job_id_03c': 9308288} |
| plugins | PluginCollection | mkdocs_quiz [MkDocsQuizPlugin], material/search [SearchPlugin], open-in-new-tab [OpenInNewTabPlugin], rss [GitRssPlugin], redirects [RedirectPlugin], awesome-nav [AwesomeNavPlugin], material/tags [TagsPlugin], git-revision-date-localized [GitRevisionDateLocalizedPlugin], macros [MacrosPlugin], llmstxt [MkdocsLLMsTxtPlugin], 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: dict = None) *Default Mkdocs-Macro*: List an object (by default the variables) ''' macros_info: ''' Function: () *Test/debug function*: list useful documentation on the mkdocs_macro environment. ''' now: ''' Function: () *Default Mkdocs-Macro*: Get the current time (at the moment of the project build). It 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) If url is relative, fix it so that it points to the docs directory. This is necessary because relative links in markdown must be adapted in html ('img/foo.png' => '../img/img.png'). ''' pages_with_tag: Function: (tag) None } | SuperDict | {'context': |
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(2026, 11, 4, 13, 52, 24, tzinfo=tzoffset(None, 46800)) |
| short_commit | str | 'cd8a5744' |
| commit | str | 'cd8a574416b8e4d5edf33e992d45491f7ea14f9b' |
| tag | str | '' |
| short_tag | str | '' |
| author | str | 'geoffreyweal' |
| author_email | str | 'geoffrey.weal@gmail.com' |
| committer | str | 'geoffreyweal' |
| committer_email | str | 'geoffrey.weal@gmail.com' |
| date_ISO | str | 'Wed Nov 4 13:52:24 2026 +1300' |
| message | str | "Add NUMA Domains page\n\nAdd a page that explains NUMA domains for researchers who are new to\ncomputers: cores and memory, near and far memory (told as a story about\nlabs and fridges), how Mahuika's nodes are split into NUMA domains, why\nit matters more on Mahuika than on a desktop, when it slows a job down,\nhow to check a job's NUMA domains, how to keep work near its data, and\nhow Slurm treats each NUMA domain as a socket.\n\nAdd five diagrams for the page, and link to it from Thread Placement and\nThread Affinity, Hardware, and VASP. Correct the VASP sentence that said\nNUMA domains contain the L3 cache, and fix the --extra-node-into typo on\nthe Thread Placement page.\n\nCo-Authored-By: Claude Opus 5.5 |
| raw | str | "commit cd8a574416b8e4d5edf33e992d45491f7ea14f9b\nAuthor: geoffreyweal |
| root_dir | str | '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo' |
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/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/docs', dest_dir = '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/public/nesi/support-docs/numa-domains', use_directory_urls = True, inclusion [InclusionLevel], name = 'MACROS', dest_uri = 'MACROS/index.html', page [Page], url = 'MACROS/', abs_src_path = '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/repo/docs/MACROS.md', abs_dest_path = '/home/runner/work/mkdocs-demo-deploy/mkdocs-demo-deploy/public/nesi/support-docs/numa-domains/MACROS/index.html' |
| children | NoneType | None |
| previous_page | NoneType | None |
| next_page | NoneType | None |
| _Page__active | bool | False |
| update_date | str | '2026-11-04' |
| canonical_url | str | 'https://docs.nesi.org.nz/MACROS/' |
| abs_url | str | '/MACROS/' |
| edit_url | str | 'https://github.com/nesi/support-docs/edit/main/docs/MACROS.md' |
| markdown | str | '**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/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] |
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). |
| relative_url | function | (path) Default Mkdocs-Macro: convert the path of any page according to MkDoc's internal logic, into a URL relative to the current page (implements the |
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) Get an attribute of an object. |
| batch | function | (value, linecount, fill_with, tmp, item) A filter that batches items. It works pretty much like |
| 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 | function | (s) Replace the characters |
| escape | function | (s) Replace the characters |
| 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 |
| 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 |
| forceescape | function | (value) Enforce HTML escaping. This will probably double escape variables. |
| format | function | (value, args, kwargs) Apply the given values to a |
| groupby | function | (args, kwargs, b) Group a sequence of objects by an attribute using Python's :func: |
| 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 |
| 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 |
| 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 |
| 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 |
| 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: |
| string | function | (s) Convert an object to a string if it isn't already. This preserves a :class: |
| 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 |
| unique | function | (args, kwargs, b) 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. |