Merge branch 'main' into handle-todos

Author: dokempf

.github/workflows/paper.yml

@@ -20,6 +20,9 @@ jobs:
       - name: Install Python requirements
         run: pip install -r requirements.txt
 
+      - name: Install LaTeX requirements for matplotlib
+        run: sudo apt install -y texlive-latex-base texlive-latex-extra cm-super-minimal texlive-fonts-extra
+
       - name: Create contributor snippet
         run: python contributors.py
 
@@ -29,8 +32,10 @@ jobs:
       - uses: xu-cheng/latex-action@v3
         with:
           root_file: paper.tex
+
       - name: move
         run: mkdir -p github_artifacts && mv ${{ env.DIR }}/*.pdf ./github_artifacts/ 
+
       - name: Upload pdf as artifact
         uses: actions/upload-artifact@v4
         with:

contributors.py

@@ -15,10 +15,17 @@
 for author in data["authors"]:
     if 'affiliations' in author:
         affiliations.extend(author["affiliations"])
-data["affiliations"] = {aff: i + 1 for i, aff in enumerate(list(dict.fromkeys(affiliations)))}
+# make sure affiliations are not duplicated - here by checking for exact name string
+affiliations = list({aff['name']: aff for aff in affiliations}.values())
+
+# create and add unique index and also a reverse lookup table
+data["affiliations"] = {i + 1: aff for i, aff in enumerate(affiliations)}
+aff_index_by_name    = {aff['name']: i for i, aff in data["affiliations"].items()}
+
+# attach index to authors
 for author in data["authors"]:
     if 'affiliations' in author:
-        author["affiliations"] = [data["affiliations"][aff] for aff in author["affiliations"]]
+        author["affiliations"] = [aff_index_by_name[aff['name']] for aff in author["affiliations"]]
 
 env = jinja2.Environment(
    loader=jinja2.FileSystemLoader(os.getcwd()),

contributors.tex.j2

@@ -8,6 +8,6 @@
 {%- for author in data.authors %}
 \author[​{% if author.affiliations %}{{ author.affiliations|join(", ") }}{% endif %}]{{ "{" }}{{ author.author }}{% if author.orcid is defined %}\texorpdfstring{\thinspace\orcidlink{ {{-author.orcid-}} }}{}{% endif %}{{ "}" }}
 {%- endfor %}
-{%- for affiliation, index in data.affiliations.items() %}
-\affil[{{ index }}]{{ "{" }}{{ affiliation }}{{ "}" }}
+{%- for index, affiliation in data.affiliations.items() %}
+\affil[{{ index }}]{{ "{" }}{{ affiliation.name }}{% if affiliation.ror is defined %}\texorpdfstring{\thinspace\rorlink{ {{-affiliation.ror-}} }} {}{% endif %}{{ "}" }}
 {%- endfor %}

contributors.yml

@@ -4,15 +4,17 @@ authors:
     lastName: Ankenbrandt
     initials: MJA
     affiliations:
-      - Center for Computational and Theoretical Biology, University of Würzburg, Germany
+      - name: Center for Computational and Theoretical Biology, University of Würzburg, Germany
+        ror: https://ror.org/00fbnyb24
     orcid: 0000-0002-6620-807X
 
   - author: "Leyla Jael Castro"
     firstName: Leyla Jael
     lastName: Castro
     initials: LC
     affiliations:
-      - Semantic Technologies team, ZB MED Information Centre for Life Sciences, Germany
+      - name: Semantic Technologies team, ZB MED Information Centre for Life Sciences, Germany
+        ror: https://ror.org/0259fwx54
     orcid: 0000-0003-3986-0510
     email: [email protected]
 
@@ -21,7 +23,8 @@ authors:
     lastName: Caspart
     initials: RC
     affiliations:
-      - Scientific Computing Center, Karlsruher Institut für Technologie, Germany
+      - name: Scientific Computing Center, Karlsruher Institut für Technologie, Germany
+        ror: https://ror.org/04t3en479
     orcid: 0000-0002-5502-9412
     tier: 1
 
@@ -30,7 +33,8 @@ authors:
     lastName: Flemisch
     initials: BF
     affiliations:
-      - Institute for Modelling Hydraulic and Environmental Systems, University of Stuttgart, Germany
+      - name: Institute for Modelling Hydraulic and Environmental Systems, University of Stuttgart, Germany
+        ror: https://ror.org/04vnq7t77
     orcid: 0000-0001-8188-620X
     email: [email protected]
     tier: 1
@@ -40,7 +44,8 @@ authors:
     lastName: Goth
     initials: FG
     affiliations:
-      - Institute for Theoretical Physics and Astrophysics, University of Würzburg, Germany
+      - name: Institute for Theoretical Physics and Astrophysics, University of Würzburg, Germany
+        ror: https://ror.org/00fbnyb24
     orcid: 0000-0003-2707-4790
     email: [email protected]
     acknowledgements: |
@@ -54,7 +59,8 @@ authors:
     lastName: Grad
     initials: JNG
     affiliations:
-      - Institute for Computational Physics, University of Stuttgart, Germany
+      - name: Institute for Computational Physics, University of Stuttgart, Germany
+        ror: https://ror.org/04vnq7t77
     orcid: 0000-0002-5821-4912
     email: [email protected]
     acknowledgements: |
@@ -73,7 +79,8 @@ authors:
     lastName: Hagdorn
     initials: MH
     affiliations:
-      - Geschäftsbereich IT, Charité Universitätsmedizin Berlin, Germany
+      - name: Geschäftsbereich IT, Charité Universitätsmedizin Berlin, Germany
+        ror: https://ror.org/001w7jn25
     orcid: 0000-0002-5076-4864
     email: [email protected]
 
@@ -82,7 +89,8 @@ authors:
     lastName: Kempf
     initials: DK
     affiliations:
-      - Heidelberg University, Scientific Software Center, Germany
+      - name: Heidelberg University, Scientific Software Center, Germany
+        ror: https://ror.org/038t36y30
     orcid: 0000-0002-6140-2332
     email: [email protected]
     acknowledgements: |
@@ -95,7 +103,8 @@ authors:
     lastName: Linxweiler
     initials: JL
     affiliations:
-      - Technische Universität Braunschweig, Germany
+      - name: Technische Universität Braunschweig, Germany
+        ror: https://ror.org/010nsgg66
     orcid: 0000-0002-2755-5087
     email: [email protected]
     tier: 1
@@ -105,7 +114,8 @@ authors:
     lastName: Loewe
     initials: AL
     affiliations:
-      - Karlsruhre Institute of Technology (KIT)
+      - name: Karlsruhre Institute of Technology (KIT)
+        ror: https://ror.org/04t3en479
     orcid: 0000-0002-2487-4744
     email: [email protected]
 
@@ -114,7 +124,8 @@ authors:
     lastName: Löffler
     initials: FL
     affiliations:
-      - Competence Center Digital Research, Friedrich Schiller University Jena, Germany
+      - name: Competence Center Digital Research, Friedrich Schiller University Jena, Germany
+        ror: https://ror.org/05qpz1x62
     orcid: 0000-0001-6643-6323
     email: [email protected]
     tier: 1
@@ -124,7 +135,8 @@ authors:
     lastName: Schäfer
     initials: PMS
     affiliations:
-      - Competence Center Digital Research, Friedrich Schiller University Jena, Germany
+      - name: Competence Center Digital Research, Friedrich Schiller University Jena, Germany
+        ror: https://ror.org/05qpz1x62
     orcid: 0000-0003-3931-6670
     email: [email protected]
     tier: 1
@@ -134,7 +146,8 @@ authors:
     lastName: Sommer
     initials: PS
     affiliations:
-      - Institute of Carbon Cycles, Helmholtz Coastal Data Center, Helmholtz-Zentrum Hereon, Germany
+      - name: Institute of Carbon Cycles, Helmholtz Coastal Data Center, Helmholtz-Zentrum Hereon, Germany
+        ror: https://ror.org/03qjp1d79
     orcid: 0000-0001-6171-7716
     email: [email protected]
 
@@ -143,7 +156,8 @@ authors:
     lastName: Speck
     initials: RS
     affiliations:
-      - Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Germany
+      - name: Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Germany
+        ror: https://ror.org/02nv7yv05
     orcid: 0000-0002-3879-1210
     email: [email protected]
     tier: 1
@@ -153,7 +167,8 @@ authors:
     lastName: Struck
     initials: AS
     affiliations:
-      - Cluster of Excellence Matters of Activity. Image Space Material at Humboldt-Universitaet zu Berlin
+      - name: Cluster of Excellence Matters of Activity. Image Space Material at Humboldt-Universitaet zu Berlin
+        ror: https://ror.org/01hcx6992
     orcid: 0000-0002-1173-9228
     email: [email protected]
     acknowledgements: |

group_composition_plot/.gitignore

@@ -1,2 +1,3 @@
 **/*.pdf
+group_composition_plot_the_fantastic_four.labels
 /submissions.volume

group_composition_plot/Makefile

@@ -8,8 +8,9 @@ all:	group_composition_plot_the_fantastic_four.pdf \
 group_composition_plot_the_fantastic_four.pdf:	submissions/2023-12-06/Friedrich_Schiller_University_Jena_2023-12-06_10-43-44.json \
 						submissions/2023-12-06/Scientific_Software_Center_2023-12-21_13-13-27.json \
 						submissions/2023-12-06/University_of_Reading_2023-12-11_10-18-14.json \
-						submissions/2023-12-06/Princeton_University_2023-11-29_18-33-21.json
-	./group_composition_plot.py --legend --outfile $@ $^
+						submissions/2023-12-06/Princeton_University_2023-11-29_18-33-21.json \
+						group_composition_plot.py
+	./group_composition_plot.py --legend --outfile $@ $(filter %.json,$^)
 
 group_composition_plot_all.pdf:	$(GOOD)
 	./group_composition_plot.py --legend --outfile $@ $^

group_composition_plot/group_composition_plot.py

@@ -1,9 +1,22 @@
 #!/usr/bin/env python3
 import sys, argparse
+import matplotlib
+rc_params = {'text.usetex': True,
+         'svg.fonttype': 'none',
+         'text.latex.preamble': r'\usepackage{libertine}',
+         'font.size': 14,
+         'font.family': 'Linux Libertine',
+         'mathtext.fontset': 'custom',
+         'mathtext.rm': 'libertine',
+         'mathtext.it': 'libertine:italic',
+         'mathtext.bf': 'libertine:bold'
+         }
+matplotlib.rcParams.update(rc_params)
 import matplotlib.pyplot as plt
 import json
 from pprint import pprint
 
+
 def errorexit(msg='internal error', code=1):
     print(msg, file=sys.stderr)
     sys.exit(code)
@@ -42,25 +55,36 @@ def errorexit(msg='internal error', code=1):
 activity_to_color = {activity: colors[i] for i, activity in enumerate(activity_names)}
 
 # Creating the joint plot
-scaling = .9
+scaling = 6
 iymax = (len(data)+1)//2
-fig = plt.figure(figsize=(scaling*16, scaling*9/2*iymax))
+fig = plt.figure(figsize=(scaling, scaling/2*iymax))
 
 i = 1
+inst_names = {}
 for inst, idata in data.items():
     ax = fig.add_subplot(iymax, min(2, len(data)), i)
-    ax.pie(idata['activity_weights'], colors=colors, startangle=140, shadow=True, radius=.8)
+    ax.pie(idata['activity_weights'], colors=colors, startangle=90, shadow=True, radius=1)
     inst_name = idata['institution_name']
     if 'group_name' in idata:
-        inst_name = idata['group_name'] + "\n" + inst_name
+        inst_name = idata['group_name'] + ", " + inst_name
     if not args['hide_titles']:
-        ax.set_title(inst_name, fontsize=20, y=-0.05)
+        ax.set_title(chr(ord('a')-1+i), y=-0.05)
+        inst_names[chr(ord('a')-1+i)] = inst_name
     i += 1
 
 # Shared legend
 if args['legend']:
-  fig.legend(activity_names, title="Activities", loc="center right", bbox_to_anchor=(1.2, 0.5), fontsize=20)
+  legend = fig.legend(activity_names, title="Activities",
+      loc="upper right", bbox_to_anchor=(1.4, .7), frameon=False)
+  #nothing = matplotlib.patches.Rectangle((0,0), 1, 1, fill=False, edgecolor='none', visible=False)
+  #legend_inst = plt.legend([nothing]*len(inst_names),
+  #                         [i+": "+inst_name for i, inst_name in inst_names.items()],
+  #    loc="upper left", bbox_to_anchor=(-1.2, 0.0), frameon=False)
+  #plt.gca().add_artist(legend_inst)
+  with open(args['outfile'].replace('.pdf', '.labels'), 'w') as f:
+      f.write(', '.join([i+": "+inst_name for i, inst_name in inst_names.items()]))
 
 plt.tight_layout()
+fig.subplots_adjust(bottom=0)
 fig.savefig(args['outfile'], bbox_inches='tight')
 # plt.show()