History#

Pipeline#

  • anHALyze: tools to spot HAL issues (bad author metadata, DBLP comparison, widget)

  • EgoConf: find your conferences/journals

  • Gismo integration: team/researcher clustering and keyword maps (word clouds shipped in 0.6.0)

  • OpenAlex source

  • Conf2Lab: build a lab from a set of publications (e.g. a conference)

0.6.1 (2026-06-29): Bug fixes#

Bug fixes#

  • BibTeX export from the graph modal — the per-node / per-edge Download .bib button and the per-entry copy button — no longer appends a stray Copy after each entry, which made the downloaded/copied BibTeX unparsable. The copy button lives inside the <pre>, so the readers now keep only its text nodes (not the button). The whole-lab export (LabMap.to_bib / menu) was already clean. No LDB format change.

Improvements#

  • make_vis() (hence LabMap.html() / show_html()) now accepts the documented interaction_options keyword. The code only read interaction_option, so passing the documented plural name raised TypeError: unexpected keyword arguments. Both names work.

0.6.0 (2026-06-29): User requests, vol. 2#

Highlights#

  • Acted on a round of real user feedback on the collaboration graphs: smarter node initials (composite first names like Jean-François Laslier → JFL, and automatic disambiguation of same-initials neighbours → JLa / JLe), uniform node sizes, a legend that now defines itself on hover, a coloured square for comets, and a one-click toggle between the astronomy vocabulary and plain-language labels.

  • New time filter: a year range-slider (from the menu) filters collaborations to a period live, recomputing nodes, edges and comets.

  • New theme menu entry to force light / dark / auto (with a theme= build option).

  • Comets are now gently pulled toward their own group’s cluster instead of scattering on the rim, while staying draggable.

Visualization#

  • initials() rewritten: keeps every initial of a composite first name (hyphen- or space-separated), skips lowercase particles (Élie de Panafieu → ÉP), and the common First Last case stays two letters. New graph-level node_labels() disambiguates authors that share initials by extending with surname letters (JLa / JLe).

  • Minimum node size (widthConstraint) so short-label nodes no longer render smaller than others. Tunable via nodes_options=.

  • Legend overhaul: every entry exposes a definition on hover; a menu entry (“Use alternative labels”) swaps the visible wording with the hover one. Each group ships a primary label (display) and an alternative (display_alt), both overridable per group. EgoMaps use people-centric wording, other labs membership-centric wording.

  • Comets get a coloured legend square (a lightened member colour) and lose the “(Singletons)” parenthesis.

  • Node-label disambiguation is length-capped (node_labels(max_len=5)) so names that cannot be told apart (e.g. a source yielding “Surname Firstname”) produce bounded labels instead of long garbage.

  • Lip6Map reorders the LIP6 directory’s “Surname Given” labels to “Given Surname”, so initials and display follow the usual convention.

  • Time-window slider (dual-handle, dependency-free) with a graceful empty state when a filter leaves nothing to show.

  • Comet gravity: invisible attractor springs added only to the rendered graph (never to the data model, so comet detection is unchanged) pull each comet toward its group.

  • Forced light/dark theme via CSS-variable overrides on the box and modal.

New features#

  • LabMap.html() / make_vis() gains a theme= argument ("auto", "light", "dark").

  • make_vis() option dicts (nodes_options, edges_options, physics, interaction_option) now merge with the defaults, so a single field can be tweaked without restating the whole dict.

  • EgoMap.build(target=None) builds an exhaustive ego map: every planet, then moons capped at moon_ratio × the number of planets (default 0.5) to avoid the thousands of authors a full moon expansion would pull in.

  • Exhaustiveness-aware wording: moons read “Most frequent collaborators” when capped and “Collaborators” when the set is complete.

  • LabMap.overrides: per-author escape hatch for scraped labs. Map an author name to "drop" (skip) or to a parenthetical source spec ("hal: key, ldb: key", "no_auto") to stop a near-homonym or a DB-sparse newcomer from grabbing someone else’s identity via fuzzy source resolution.

  • Keyword clouds: LabMap.wordcloud(query=, group=) and LabMap.keywords(...) extract weighted keywords for a topic, an author, a group, or the whole lab, via a new GismoLab (authors ↔ words cross-embedding over titles + abstracts). Pass gismo_lab= to reuse a prebuilt instance across many queries instead of rebuilding each call. A group’s keywords aggregate the text of all its publications (word-space), so the cloud reflects the group’s actual output instead of giving low-output authors disproportionate weight. A large curated English + French + scraping-noise stop-word list keeps the clouds clean. WordCloud renders a self-contained HTML cloud (_repr_html_ in notebooks, save_html to a file). Near-duplicate n-grams are merged (“p2p” absorbed by “p2p networks”). No new dependency (built on Gismo).

Documentation#

  • FAQ: fixed a typo (“a package base on” → “based on”); new entry explaining why a real collaborator can show up grey (a co-publication recorded under a different author identity) and how to fix it from the source side.

LDB / internals#

  • New ZList storage format: each frame stores individually-pickled items behind an offset index, so random access unpickles a single item instead of the whole frame, and an optional zstd dictionary can be trained for tighter compression. build_db now does a two-pass build — a fast dict-less streaming pass, then ZList.optimize() repacks into small dict-compressed frames (10 publications / 20 authors per frame) for much smaller dumps and cheaper access. optimize() / estimated_uncompressed_size() also return a plain list when the data is small enough that memory is not a concern.

  • The LDB asset format changed: the ldb.pkl.zst shipped with this release is rebuilt; older local caches are incompatible and are re-fetched automatically on first use (LDB.retrieve() to force it).

  • build_db logs each phase, including the two-pass optimize (dictionary training + level-19 recompression); python -m gismap.build configures timestamped logging so build phases and their durations are visible in CI.

Robustness#

  • gismap.utils.requests.get() now passes a connect/read timeout (and retries on timeout), so a slow or hung endpoint no longer blocks a scrape (or the test suite) indefinitely.

  • AlgoRes2016 reads through the archive.org mirror: the live LaBRI page has a ~20 s cold-cache penalty on first hit; the mirror serves byte-identical content in ~2 s and is more durable for a long-dead conference site.

CI / build#

  • The ldb-build workflow uploads the rebuilt ldb.pkl.zst to the release that matches the built version (derived from gismap.__version__), aborting if that release does not exist, instead of always clobbering the latest release. A ref input rebuilds a specific release’s asset (e.g. v0.5.4) with the current workflow logic.

  • Author / publication counts in the verify step are read straight from the dump instead of via load_db(), which used to rebuild the search engine and re-dump the asset — silently re-inflating a --no-search asset.

  • Progress bars are throttled in CI (TQDM_MININTERVAL) so logs stay readable.

0.5.4 (2026-05-04): Some user requests#

Highlights#

  • BibTeX export everywhere: per-publication [.bib] toggle in the modal, per-author / per-pair “Download .bib” buttons, and a whole-lab download via the new menu (or programmatically via LabMap.to_bib()).

  • Reorganized graph controls: a hamburger menu (top-left) groups Redraw, Full Screen, Show/Hide Legend, PNG export, and the lab-level .bib export. Full Screen becomes a YouTube-style icon at the bottom-right.

  • Modal overlay is finally legible in Jupyter dark mode.

  • HTML produced by lab.html() / save_html() is ~4× smaller for typical labs.

  • New programmatic exports: LabMap.to_bib(), LabMap.to_json(), LabMap.to_csv().

  • New tutorial HALTools: walk-through of diff_sources() and find_duplicates() on four real-world researcher profiles, with an explicit “what to act on, what to ignore” wrap-up. Replaces and expands the former Analyzing sources section of the EgoMap tutorial.

Visualization#

  • New hamburger menu (top-left) replacing the standalone Redraw button. Single entry point for: Redraw, Full Screen, Show/Hide Legend, Download <lab>.bib (whole-lab BibTeX), Download PNG, Copy PNG to clipboard. The <lab> label always matches the actual downloaded filename.

  • PNG export of the collaboration graph (download or copy to clipboard). The legend is composited natively to canvas — no external dependency, no perceptible delay.

  • Full Screen icon (bottom-right, expand/compress glyph in YouTube style) replaces the text button. Tooltip and the matching menu entry switch between “Full Screen” and “Exit Full Screen” automatically.

  • Per-publication [.bib] toggle in the modal overlay reveals an inline <pre> with the BibTeX entry. A sphinx_copybutton-style copy button (revealed on hover) sits in the top-right of each <pre>.

  • Per-publication [abstract] toggle for publications that carry an abstract (HAL).

  • Per-list “Download .bib” button (author or author-pair) now sits right-aligned on the same line as the “Publications of …” / “Joint publications from …” header (used to wrap to a new line below).

  • All overlay button handling uses event delegation on the modal body — no per-click listener attachment.

New features#

  • Add LabMap.to_bib(name=None, query=None) to export a lab’s publications as a BibTeX file. Optional query argument reuses select_publications to filter (string match, fuzzy title, or callable).

  • Add LabMap.to_json(name=None) and LabMap.to_csv(name=None). CSV produces two files (<name>_authors.csv, <name>_publications.csv).

  • Add pub_to_bibtex(pub) in gismap.sources.bibtex for per-publication BibTeX rendering (handles all Publication subclasses including SourcedPublication with note = {Also at: …} for non-primary source URLs).

  • Add to_dict() on Author, Publication, SourcedAuthor, SourcedPublication, and LabAuthor for JSON-friendly serialization.

  • Tuning kwargs on LabMap.__init__: max_co_authors, min_title_words, taboo_words, taboo_authors. Subclasses can adjust default filters without mutating publication_selectors by index.

  • LaasMap/LaasFull (gismap.lab_examples.toulouse) gain department_level to label authors by parent department; LaasFull gains with_support to include LAAS support services and deduplicates authors appearing in multiple teams.

Documentation#

  • New tutorial docs/tutorials/haltools.ipynb covering diff_sources() and find_duplicates() end-to-end (clean profile, messy profile, duplicate-heavy profile, and pid-vs-fullname diagnosis). Wired into docs/tutorials/index.md and the FAQ Binder list.

  • The haltools notebook is shipped with stored outputs on purpose: the analysis text references specific HAL/LDB items, so a stale narrative would be worse than a slightly stale snapshot. Re-execute locally before each release.

  • Removed the Analyzing sources section from docs/tutorials/egomap.ipynb (now superseded by the dedicated tutorial).

  • New ## Exporting a lab section in docs/tutorials/lab_tutorial.ipynb showing to_bib() (whole-lab and query=-filtered), to_json(), and to_csv().

  • Updated lab_tutorial’s “Few things about the generated graph” enumeration to describe the hamburger menu, the bottom-right Full Screen icon, and the in-modal [.bib] / [abstract] / “Download .bib” affordances.

  • Refreshed the FAQ: the graph is spinning and it’s too small recipes now refer to the new menu and icon (Redraw is now a menu entry, not a standalone button); the publication should be there in my LabMap section leads with the new constructor kwargs (max_co_authors, min_title_words, taboo_words, taboo_authors) and keeps publication_selectors as the advanced escape hatch.

Improvements#

  • HTML output is ~4× smaller for typical labs. Each publication is now shipped once in a shared JS dict and referenced by key from nodes and edges; the modal is rendered on click from that dict, instead of inlining the full publication HTML once per author and once per author-pair. Internal refactor of gismap.gisgraphs.graph and gismap.gisgraphs.js.

  • LAAS_TABOO now extends editorials instead of duplicating it.

  • Docstrings completed on LaasMap, LaasFull, and LabMap (full Parameters sections).

  • LabMap.save_html() and the new export methods raise ValueError if neither name= nor self.name is set, instead of crashing on Path(None).

  • LDB cache is now stored under a Python-version-specific subdirectory (<user_data_dir>/gismap/py{X.Y}/ldb.pkl.zst) so that running gismap from multiple Python interpreters on the same machine no longer leads to mutually corrupted dumps. Users with several Python versions will pay one (re-)retrieve per interpreter; mono-Python users see no change other than the new path.

CI#

  • Network-heavy tests now run only on the 3.12 matrix runner (the one that feeds Codecov). The 3.11 / 3.13 / 3.14 runners skip them via --ignore. Two test paths are concerned: gismap/sources/dblp.py (live DBLP doctests) and tests/test_lab_examples.py (live scraping of irif.fr / lamsade / lincs / laas). With four runners hitting the same endpoints in parallel, the remote side would issue temporary bans, and the suite would stall for ~20 min on exponential backoff before +FLAKY downgraded DBLP failures to skips, or test_lab_examples failed outright on a ConnectionError. Live-network coverage is preserved on 3.12.

Bug fixes#

  • Modal overlay was unreadable in Jupyter dark mode (fixed-light card on dark canvas). Modal colors now resolve through var(--pst-color-…, var(--jp-…, fallback)) chains so the modal follows the host theme.

  • Harden JSON embedded inside <script>: any </ (e.g. </script> inside a publication title) is rewritten to <\/, neutralizing a tag-breakout vector.

  • Fix LaasMap._author_iterator department-level scraping: find("p", {"class", "font11"}) (a set) was silently wrong; replaced by {"class": "font11"} (a dict).

  • Fix LDB._initialized = True being set even when search_engine was None (e.g. interrupted download leaving the GitHub release pickle as-is, or pre-existing dump from a previous build). Subsequent search_author() calls then crashed with AttributeError: 'NoneType' object has no attribute 'extract'. LDB.load() now rebuilds and re-dumps the search engine whenever the loaded state has none.

  • LDB._download_file now writes through safe_write (temp file + atomic rename) so an interrupted download no longer leaves a partial ldb.pkl.zst that the next run would try to load.

0.5.3 (2026-04-09): HALTools v1#

New features#

  • Add diff_sources() to compare publications between two databases or search strategies

  • Add find_duplicates() to find duplicate publications within a single database

  • Add select_publications() method for querying publications of a lab by fuzzy title match, key, or callable filter

  • Add del_publication() method for removing publications from a lab with optional confirmation

Improvements#

  • Add __str__ and __repr__ to LabMap, EgoMap, Author, and Publication for human-readable display

  • EgoMap automatically uses the star’s name when no name is provided

  • Fix Publication.__str__ to avoid double period when title ends with “.”

  • Fix misleading tqdm progress in expand(): progress bar now reflects actual work (network calls) instead of completing instantly

  • Add format_authors() utility with Oxford comma formatting (sources/models.py)

  • Use format_authors() in publication overlays (gisgraphs/graph.py)

  • auto_sources now completes missing DBs instead of being all-or-nothing: specifying a HAL key no longer prevents automatic LDB discovery

  • Add hal:fullname shorthand to force HAL name-based search (useful when pid is too restrictive)

  • Add no_auto flag in parentheses notation to disable automatic source completion

  • Add Publication.short_str() for compact one-line display with URL

  • Add SourcedPublication.url property (delegates to first source with a URL)

Bug fixes#

  • Fix comets (singletons) legend: checkbox visibility is now fully dynamic, appearing only when singletons exist for the current group selection

  • Fix HALAuthor.check_cv(): adapt CV page detection to current HAL markup (soup.main.section instead of soup.form), and catch AttributeError in image extraction

  • Fix LDB.search_author() returning duplicate entries when aliases normalize to the same name; deduplicate at index build time and at query time

  • Fix regroup_publications() partition bug: a publication matching two groups could appear in both instead of just the first

0.5.2 (2026-04-06)#

New features#

  • Add add_publication() method to manually add publications to a lab with fuzzy author matching

  • New Manual database backend with Outsider and Informal classes (sources/manual.py)

  • New similarity_matrix() utility for unified fuzzy matching (utils/fuzzy.py)

Improvements#

  • Replace domonic with f-strings in gisgraphs/, removing domonic + 4 transitive dependencies

  • Fix slow import (~4.1s → ~0.2s): lazy imports for bof.fuzz, GismapWidget, LDB, gismo

  • Refactor expansion: proper_prospects() returns a simple list, labify_publications replaced by regroup_authors

  • Add version compatibility warning when loading an LDB built for a different gismap version

CI/CD#

  • Parallelize notebook execution in docs CI (matrix strategy, per-notebook cache, shared LDB cache)

  • Add LDB cache to build CI (per Python version), simplify workflows (remove setup-python, enable uv cache)

Tests#

  • Add parametrized tests for lab_examples _author_iterator() (6 labs)

  • Improve test coverage (81% → 83% lines, 61% → 64% branches)

  • Fix lazy import regression: db_dict() forces backend imports before discovery

Documentation#

  • Document LDB management workflow in FAQ

  • Simplify “Adding publications” tutorial with add_publication()

0.5.1 (2026-03-30)#

  • Fix publication deduplication: fingerprint now combines title and authors (normalized) instead of title only, preventing incorrect merges of different papers with similar titles

  • Switch vis-network CDN from unpkg to jsDelivr (CORS fix for JupyterLab)

  • Enable Light-themed full screen (previously, full screen was always dark)

  • Slight adjustment in legend alignment

  • IRIF added to the gallery

  • Adapt Lamsade authors retrieval to new webpage format

  • Add ruff linter configuration and pre-commit hooks

  • Fix all existing ruff findings (import sorting, pyupgrade, line length)

  • Consolidate coverage configuration into pyproject.toml

  • Bump ipykernel minimum to 7.x

  • Upgrade CI tooling: uv 0.11.0, Codecov v5, Pandoc 3.9

  • Fix potential circular import in lab_author.py (lazy db_dict lookup)

  • GH actions: cached gallery (tricky)

0.5.0 (2026-02-14)#

  • BREAKING CHANGE LDB now supports aliases (old assets not compatible)

  • Algotel/Cores added to the gallery

  • Add throttling to HAL requests, as they apparently started to limit the traffic

0.4.1 (2026-02-02): Python 3.14 support#

  • Add Python 3.14 compatibility (requires gismo>=0.5.4).

  • Drop Python 3.10 support (now requires 3.11+).

  • LDB search engine fine-tuned.

  • Various typo fixes.

0.4.0 (2026-01-27): Local DB#

New DB: LDB (Local DB). All the strengths of DBLP, None of its weaknesses.

  • Convert the whole DBLP relational DB into a Gismap compatible local object.

  • Introduces new compressed list format (Zlist) to keep the DB in memory.

  • Use Bag-of-Factors to enable approximate search.

  • You can build your own dataset or just rely on the one we provide and update.

Also, Lamsade added to the gallery.

0.3.1 (2025-11-27): Bug fixes#

  • Fix BS4 dependency issue.

  • Errors in readme

0.3.0 (2025-11-25): Bigger, faster, prettier#

  • VisJS integration has been fully revamped to reduce JS errors and resource consumption.

  • A gallery is now available in the documentation to showcase the possibilities:

    • Lip6 (Sorbonne university CS lab, single team / whole lab);

    • Laas (Toulouse university CS lab, single team / whole lab) + Solace (collab team);

    • Cédric (CNAM, whole CS Lab);

    • LINCS (legacy Paris-based collaboration project).

  • Binder integration: you can now play with GisMap directly in your browser, no local Python required!

  • A FAQ, because when the developer (me) starts to forget some how-tos, you know it’s time for a FAQ.

  • GisGraphs can now have groups with automatic color selection and a selectable legend.

  • Gradient-based coloring for inter-group edges (that one was no picnic).

  • Lots of minor improvements here and there.

0.2.2 (2025-09-08): Various upgrades#

  • Breaking change: renaming some methods/attributes (e.g. sun is now star in EgoMap)

  • Graphs now include unconnected non-empty nodes (their display will be an option in the next version)

  • Typos here and there

  • New Lab class: LINCS

0.2.1 (2025-09-01): Minor VisJS enhancements#

  • Better handling of dark/light mode (should be compatible with Pydata, Jupyter, and System).

  • Responsive size

0.2.0 (2025-08-31): EgoMaps!#

  • New lab structure: EgoMap shows the people that revolve around you!

  • New lab method: expansion, which adds moons (neighbor researchers).

  • Add filters when building authors and publications.

  • Physics engine changed for better visualization.

  • Multi-source handling fine-tuned.

  • Better display (size and theme).

0.1.0 (2025-07-24): First release#

  • First release on PyPI.

  • Online DBLP and HAL DB implemented.

  • Lab structures implemented.

  • Early version of collaboration graph available.