diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index e4d2b0d..5341d07 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -17,8 +17,10 @@ concurrency: jobs: build: - runs-on: ubuntu-22.04 + runs-on: ubuntu-22.04 + #if: ${{ github.event.workflow_run.conclusion == 'success' }} + steps: - uses: actions/checkout@v3 - uses: r-lib/actions/setup-r@v2 diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 22ba276..8ff783a 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -1,9 +1,9 @@ name: check -on: - push: - paths: - - "staff/**.yaml" +on: push +# push: +# paths: +# - "trombinoscope/staff/**" concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} diff --git a/.github/workflows/check_scripts/check_yaml.py b/.github/workflows/check_scripts/check_yaml.py index 5b1d935..1d0ba26 100755 --- a/.github/workflows/check_scripts/check_yaml.py +++ b/.github/workflows/check_scripts/check_yaml.py @@ -15,7 +15,6 @@ def validate_category(d,f): def check_bibtex_file(d, f): p = pathlib.Path(f).parent.parent / 'publication' - print(p) if 'bibtex' in d and d['bibtex']: return (p / d['bibtex']).exists() return True @@ -31,12 +30,17 @@ def validate_orcid(d, f): def validate_url(d, f): regex = re.compile(r'^https?://') - try: - if re.search(regex, d['homepage']): - return False - except Exception: + if 'homepage' in d.keys(): + if d['homepage'] is not None: + if re.search(regex, d['homepage']): + return True + else: # case value do not follow specification + return False + else: # case no value provided for homepage tag + return True + else: # case no homepage tag return True - return True + diff --git a/.github/workflows/check_scripts/images_exist.sh b/.github/workflows/check_scripts/images_exist.sh index d162cb9..4c5fbb0 100755 --- a/.github/workflows/check_scripts/images_exist.sh +++ b/.github/workflows/check_scripts/images_exist.sh @@ -12,9 +12,9 @@ awk '/^[[:blank:]]*image: / { if [[ $ymlfile == *TEMPLATE* ]]; then continue fi + imgfile=$(tr -dc '[[:print:]]' <<< "$imgfile") # remove non printable character if [ ! -e "$imgfile" ]; then - printf '%s (from %s) does not exist\n' \ - "$imgfile" "$ymlfile" >&2 + echo "Achtung: $imgfile (from $ymlfile) does not exist\n" >&2 success=false fi done diff --git a/trombinoscope/staff/TEMPLATE.yaml b/trombinoscope/staff/TEMPLATE.yaml index 5700618..f84b3e8 100644 --- a/trombinoscope/staff/TEMPLATE.yaml +++ b/trombinoscope/staff/TEMPLATE.yaml @@ -38,7 +38,7 @@ workplace: XXX University # affiliation: CNRS/INRAE/etc # -# The SouthGreen facility that you are part of. +# The SouthGreen facility that you are part of. # facility: iTrop # diff --git a/trombinoscope/staff/alexis-dereeper.yaml b/trombinoscope/staff/alexis-dereeper.yaml index 966d924..b2b1274 100644 --- a/trombinoscope/staff/alexis-dereeper.yaml +++ b/trombinoscope/staff/alexis-dereeper.yaml @@ -38,7 +38,7 @@ workplace: IRD Montpellier # affiliation: IRD # -# The SouthGreen facility that you are part of. +# The SouthGreen facility that you are part of. # facility: SouthGreen # @@ -47,7 +47,7 @@ facility: SouthGreen # proteomics, software, statistics, structure, systems biology, # dataservices, administration # -category: +category: - development - pathogen genomics - plant genomics @@ -78,7 +78,7 @@ keywords: - perl - python - rnaseq - - variants + - variants - SNP # # "role:" is the role that you play within your infrastructure. diff --git a/trombinoscope/staff/gaetan-droc.yaml b/trombinoscope/staff/gaetan-droc.yaml index a32e822..f703e0a 100644 --- a/trombinoscope/staff/gaetan-droc.yaml +++ b/trombinoscope/staff/gaetan-droc.yaml @@ -1,5 +1,4 @@ - ---- +--- staffname: Gaetan Droc type: staff @@ -12,25 +11,25 @@ phone: xxx-xxx xx xx city: - Montpellier - + workplace: AGAP Unit affiliation: CIRAD facility: SouthGreen -category: +category: - development - software - annotation - genomics - management - + bibtex: gaetan-droc.bib orcid: 0000-0003-1849-1269 -image: gaetan-droc.png +image: gaetan-droc.jpg keywords: - genome annotation @@ -39,14 +38,13 @@ keywords: - reproductible research - postgreql - web developpment - + role: Bioinformatician bio: Research engineer in Bioinformatics, part of SouthGreen sterring comittee. - My work involves NGS data analysis, including genome assembly, genome annotation, - comparative genomics, methylation analysis, and Cut&Tag, using Snakemake. - I actively participate in the development Genomes Hub through the integration of - omics data such as banana, rice, sugarcane, vanilla, coffea, cocoa. - - + My work involves NGS data analysis, including genome assembly, genome + annotation, comparative genomics, methylation analysis, and Cut&Tag, using + Snakemake. I actively participate in the development Genomes Hub through the + integration of omics data such as banana, rice, sugarcane, vanilla, coffea, + cocoa. diff --git a/trombinoscope/staff/jacques-dainat.yaml b/trombinoscope/staff/jacques-dainat.yaml index 6c6b762..4912a5b 100644 --- a/trombinoscope/staff/jacques-dainat.yaml +++ b/trombinoscope/staff/jacques-dainat.yaml @@ -28,6 +28,6 @@ category: phone: +33 (0)00 00 00 00 city: - Montpellier -affiliation: IRD-UM-CNRS +affiliation: IRD workplace: IRD facility: SouthGreen diff --git a/trombinoscope/staff/mathieu-rouard.yaml b/trombinoscope/staff/mathieu-rouard.yaml index 74e34b0..b6569c3 100644 --- a/trombinoscope/staff/mathieu-rouard.yaml +++ b/trombinoscope/staff/mathieu-rouard.yaml @@ -1,32 +1,32 @@ ---- -staffname: Mathieu Rouard -type: staff -bio: - Research scientist in Bioinformatics, part of SG sterring comittee - I am involved in genome analyses and contribute to related - web resources development. Strong focus on banana and genetic diversity. - -active: true -email: m.rouard@cgiar.org -phone: xxx-xxx xx xx -city: - - Montpellier -workplace: Alliance Bioversity and CIAT -affiliation: Bioversity International - UMR AGAP -facility: SouthGreen -category: -- genomics -- software -- management -bibtex: mathieu-rouard.bib -orcid: 0000-0003-0284-1885 -image: mathieu-rouard.jpg -keywords: - - Genome Hubs - - Banana Genomes - - Orthology - - Gene families - - rnaseq - - Gigwa - - Interoperability -role: Comité de pilotage +--- +staffname: Mathieu Rouard +type: staff +bio: + Research scientist in Bioinformatics, part of SG sterring comittee + I am involved in genome analyses and contribute to related + web resources development. Strong focus on banana and genetic diversity. + +active: true +email: m.rouard@cgiar.org +phone: xxx-xxx xx xx +city: + - Montpellier +workplace: Alliance Bioversity and CIAT +affiliation: Bioversity International - UMR AGAP +facility: SouthGreen +category: + - genomics + - software + - management +bibtex: mathieu-rouard.bib +orcid: 0000-0003-0284-1885 +image: mathieu-rouard.jpg +keywords: + - Genome Hubs + - Banana Genomes + - Orthology + - Gene families + - rnaseq + - Gigwa + - Interoperability +role: Comité de pilotage diff --git a/trombinoscope/staff/pierre-larmande.yaml b/trombinoscope/staff/pierre-larmande.yaml index 132d3b7..d1553f0 100644 --- a/trombinoscope/staff/pierre-larmande.yaml +++ b/trombinoscope/staff/pierre-larmande.yaml @@ -11,7 +11,7 @@ # # Your real name, the exact way that you want it displayed. # -staffname: Pierre Larmande +staffname: Pierre Larmande # # Most people will have "type: staff", but some may be "affiliate". # @@ -38,7 +38,7 @@ workplace: IRD Montpellier # affiliation: IRD # -# The SouthGreen facility that you are part of. +# The SouthGreen facility that you are part of. # facility: SouthGreen # @@ -47,9 +47,9 @@ facility: SouthGreen # proteomics, software, statistics, structure, systems biology, # dataservices, administration # -category: +category: - development - - annotation + - annotation - dataservices - systems biology # @@ -64,7 +64,7 @@ bibtex: pierre-larmande.bib # # If you have an ORCID ID ("NNNN-NNNN-NNNN-NNNN") # -orcid: 0000-0002-2923-9790 +orcid: 0000-0002-2923-9790 # # The name of an image file in the "img" subdirectory, no more than # about 400 pixels wide and less than 200 KB in file size. @@ -84,16 +84,18 @@ keywords: # # "role:" is the role that you play within your infrastructure. # -role: Researcher +role: Researcher # bio: - Pierre Larmande is senior researcher at IRD, the French Public Research Institute for Sustainable Development. He is member of the DIADE Unit in Montpellier. His main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data for plant genomics. - - - He obtained PhD in Informatics from the university of Montpellier in 2007 (about federated plant data integration approaches applied to agronomy) and recently obtained the habilitation to conduct research supervision (HDR) in 2020. He coordinated the Oryza Tag Line phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice database. - - - Pierre Larmande is the lead PI of the Agronomic Linked Data project (AgroLD), which is a Knowledge Graph database that consists of data integrated from a variety of plant resources and ontologies. - - - + Pierre Larmande is senior researcher at IRD, the French Public Research + Institute for Sustainable Development. He is member of the DIADE Unit in + Montpellier. His main research interests are Data integration, Semantic Web, + plant-ontologies, semantic data linking, Knowledge management and Big Data + for plant genomics. He obtained PhD in Informatics from the university of + Montpellier in 2007 (about federated plant data integration approaches + applied to agronomy) and recently obtained the habilitation to conduct + research supervision (HDR) in 2020. He coordinated the Oryza Tag Line + phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice + database. Pierre Larmande is the lead PI of the Agronomic Linked Data project + (AgroLD), which is a Knowledge Graph database that consists of data + integrated from a variety of plant resources and ontologies. diff --git a/trombinoscope/staff/valentin-guignon.yaml b/trombinoscope/staff/valentin-guignon.yaml index ed73e6a..ec06cef 100644 --- a/trombinoscope/staff/valentin-guignon.yaml +++ b/trombinoscope/staff/valentin-guignon.yaml @@ -10,9 +10,9 @@ workplace: Alliance Bioversity and CIAT affiliation: Bioversity International - UMR AGAP facility: SouthGreen category: -- software -- development -- genomics + - software + - development + - genomics homepage: https://fr.linkedin.com/in/valentin-guignon orcid: 0000-0003-0903-6811 image: valentin-guignon.jpg @@ -45,4 +45,4 @@ bio: (BrAPI, Gigwa, MGIS, Banana Genome Hub, GenoRing, GreenPhyl, Tripal,...). I am currently part of the Tripal Advisory Committee and the BrAPI Advisory Board. I have strong knowledge in databases and web development with an expertise on - the Drupal CMS. I design algorithms, methodologies and software. \ No newline at end of file + the Drupal CMS. I design algorithms, methodologies and software.