gismap 0.1.0__tar.gz → 0.2.0__tar.gz

gismap-0.2.0/.gitattributes

@@ -0,0 +1 @@
+*.ipynb filter=nbstripout

{gismap-0.1.0 → gismap-0.2.0}/.github/workflows/build.yml

@@ -17,6 +17,7 @@ env:
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     strategy:
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
@@ -33,7 +34,7 @@ jobs:
     - name: Set up uv
       uses: astral-sh/setup-uv@v5
       with:
-        version: "0.7.2"
+        version: "0.8.12"
 
     - name: Run tests
       run: |

{gismap-0.1.0 → gismap-0.2.0}/.github/workflows/docs.yml

@@ -12,12 +12,14 @@ on:
 jobs:
   build-and-deploy:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
 
       - name: Checkout
         uses: actions/checkout@v4
         with:
           persist-credentials: false
+          lfs: true
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -27,7 +29,7 @@ jobs:
       - name: Set up uv
         uses: astral-sh/setup-uv@v5
         with:
-          version: "0.7.13"
+          version: "0.8.12"
 
       - name: Setup Pandoc
         uses: pandoc/actions/setup@v1

{gismap-0.1.0 → gismap-0.2.0}/.github/workflows/release.yml

@@ -8,6 +8,7 @@ jobs:
   publish:
     name: Publish Python Package
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     environment:
       name: pypi
     permissions:
@@ -20,7 +21,7 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v5
         with:
-          version: "0.7.2"  # Pin to specific uv version
+          version: "0.8.12"  # Pin to specific uv version
 
       - name: Build package
         run: uv build --no-sources  # Recommended for production builds

gismap-0.2.0/HISTORY.md

@@ -0,0 +1,24 @@
+# History
+
+## Roadmap
+
+- Offline DBLP
+- Customized collaboration graphs
+  - Colors and size
+  - Groups
+
+## 0.2.0 (2025-08-31): EgoMaps!
+
+- New lab structure: EgoMap, an auto-lab that revolves around you!
+- New lab method: expansion, which adds *moons* (neighbor reasearchers).
+- Add filters when building authors and publications.
+- Physic engine changed fo better visualization.
+- Multi-source handling fine-tuned.
+
+
+## 0.1.0 (2025-07-24): First release
+
+- First release on PyPI.
+- Online DBLP and HAL DB implemented.
+- Lab stuctures implemented.
+- Early version of collaboration graph available.

{gismap-0.1.0 → gismap-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gismap
-Version: 0.1.0
+Version: 0.2.0
 Summary: GISMAP leverages DBLP and HAL databases to provide cartography tools for you and your lab.
 Project-URL: Repository, https://github.com/balouf/gismap
 Project-URL: Documentation, https://balouf.github.io/gismap
@@ -11,6 +11,8 @@ License-File: AUTHORS.md
 Requires-Python: >=3.10
 Requires-Dist: bof>=0.3.5
 Requires-Dist: gismo>=0.5.2
+Requires-Dist: ipykernel>=6.30.1
+Requires-Dist: tqdm>=4.67.1
 Description-Content-Type: text/markdown
 
 # Generic Information Search: Mapping and Analysis of Publications

{gismap-0.1.0 → gismap-0.2.0}/docs/conf.py

@@ -45,6 +45,17 @@ extensions = [
     "sphinx.ext.githubpages",
 ]
 
+# Remote NB execution
+nbsphinx_execute = 'always'
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', 'pdf'}"
+]
+
+def setup(app):
+    app.add_css_file("https://unpkg.com/vis-network/styles/vis-network.min.css")
+    app.add_js_file("https://unpkg.com/vis-network/standalone/umd/vis-network.min.js")
+
+
 # Smart code copy
 copybutton_exclude = ".linenos, .gp, .go"
 

{gismap-0.1.0 → gismap-0.2.0}/docs/reference/lab.md

@@ -36,3 +36,10 @@ Management of a group of people and their publications is made with the {class}`
 .. automodule:: gismap.lab.vis
     :members:
 ```
+
+## Expansion
+
+```{eval-rst}
+.. automodule:: gismap.lab.expansion
+    :members:
+```

gismap-0.2.0/docs/tutorials/egomap.ipynb

@@ -0,0 +1,218 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# EgoMap"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": [
+    "Every researcher is the center of her own universe. With EgoMaps, everyone can visualize that universe!\n",
+    "\n",
+    "Concretely, your EgoMap is a co-publication graph containing:\n",
+    "\n",
+    "- The *sun*, i.e. you, the center of the universe\n",
+    "- The *planets*, i.e. your co-authors\n",
+    "- The *moons*, e.g. the co-authors of your co-authors\n",
+    "\n",
+    "By default, EgoMaps comprise up to 50 researchers, selecting first planets, then moons."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "## Simple case"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3",
+   "metadata": {},
+   "source": [
+    "For basic scenarios, you just need to enter the name of the researcher. For example:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gismap.lab import EgoMap as Map\n",
+    "celine = Map(\"Céline Comte\")\n",
+    "celine.build()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "You can display your EgoMap with `show_html` and save it with `save_html`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "celine.show_html()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7",
+   "metadata": {},
+   "source": [
+    "## Adjusting the size"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8",
+   "metadata": {},
+   "source": [
+    "Depending on your degree, you may want to adjust the size of your universe with `target`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fabien = Map(\"Fabien Mathieu\")\n",
+    "fabien.build(target=70)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fabien.show_html()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "11",
+   "metadata": {},
+   "source": [
+    "## Using specific DBs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12",
+   "metadata": {},
+   "source": [
+    "You can specify the DB(s) you want to use. For example, if you are a French researcher not working in computer science, HAL is enough."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mathilde = Map(\"Mathilde Labbé\", dbs=\"hal\")\n",
+    "mathilde.sun.metadata.img = \"https://0.academia-photos.com/282997/7894577/15068468/s200_mathilde.labbe.jpg\"\n",
+    "mathilde.build(target=25)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mathilde.show_html()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "15",
+   "metadata": {},
+   "source": [
+    "## Filtering"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "16",
+   "metadata": {},
+   "source": [
+    "EgoMaps have default filters that try to prevent data pollution. For example, it filters out:\n",
+    "\n",
+    "- Publications with too many authors. They are usually not relevant in fields like computer science.\n",
+    "- Publications that look like editorials.\n",
+    "\n",
+    "Filters can customized. \n",
+    "For example, this publication about horse locomotion is wrongly referenced in DBLP:\n",
+    "https://dblp.org/rec/journals/sensors/PasquietBTDDF22.html\n",
+    "\n",
+    "It can be discarded by ignoring all publications about horses."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gismap.lab.filters import publication_taboo_filter\n",
+    "fanfan = Map(fabien.authors['fradurand'])\n",
+    "fanfan.publication_selectors.append(publication_taboo_filter(\"Horse\"))\n",
+    "fanfan.build(target=25)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fanfan.show_html()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{gismap-0.1.0 → gismap-0.2.0}/docs/tutorials/index.md

@@ -2,4 +2,5 @@
 
 :::{toctree}
 lab_tutorial
+egomap
 :::

gismap-0.2.0/docs/tutorials/lab_tutorial.ipynb

@@ -0,0 +1,327 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# LabMaps"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": [
+    "## Lab authors"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "Lab authors are the main ingredient to analyse a single lab (i.e. a group of researchers). You can create one just with a name and then automatically ask to retrieve the DB endpoints for this author."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gismap.lab import LabAuthor\n",
+    "maria = LabAuthor(\"Maria Potop\")\n",
+    "maria.auto_sources()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "We see a warning here. Let's look at the sources:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "maria.sources"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6",
+   "metadata": {},
+   "source": [
+    "This is actually normal: Maria has multiple identities in Hal. The warning is there to tell there is a possibility of homonyms but that is not the case here. Note that an author can have many names."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "maria.aliases"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8",
+   "metadata": {},
+   "source": [
+    "When using `auto_source`, you can tell which DBs should be uses (only online DBLP and HAL are available right now)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gismap.sources.hal import HAL\n",
+    "celine = LabAuthor(\"Céline Comte\")\n",
+    "celine.auto_sources(dbs=[HAL])\n",
+    "celine.sources"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "10",
+   "metadata": {},
+   "source": [
+    "When the sources of an author are set one can retrieve her publications."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "[p for p in celine.get_publications().values() if p.year == 2021]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12",
+   "metadata": {},
+   "source": [
+    "Lab authors can have metadata that can be used for display and further analysis but we will not cover that in this tutorial."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "13",
+   "metadata": {},
+   "source": [
+    "## Your first lab"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "14",
+   "metadata": {},
+   "source": [
+    "In GISMAP, a Lab is a class whose instances have three methods:\n",
+    "\n",
+    "- `update_authors` automatically refresh the members of the lab. It is useful at creation or when a lab evolves.\n",
+    "- `update_publications` makes a full refresh of the publications of a lab. All publications from lab members are considered (temporal filtering may be enabled later).\n",
+    "- `expand` adds *moons*, i.e. additional researchers that gravitate around the lab.\n",
+    "\n",
+    "The simplest usable subclass of Lab is `ListLab`, which uses a list of names. For example, consider the executive committee of the LINCS."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gismap.lab import ListLab\n",
+    "lab = ListLab(author_list=['Tixeuil Sébastien', 'Kofman Daniel', 'Baccelli François', 'Noirie Ludovic', 'Bassi Francesca'], name='toy_example')\n",
+    "lab.update_authors()\n",
+    "lab.authors"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "16",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lab.update_publis()\n",
+    "len(lab.publications)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "17",
+   "metadata": {},
+   "source": [
+    "Labs can be saved to you don't have to re-update them all the time."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lab.dump(lab.name, overwrite=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "19",
+   "metadata": {},
+   "source": [
+    "When you have a populated lab, you can produce a standalone HTML of the collaboration graph with `save_html`. That graph is a standalone HTML that can be displayed in a notebook or saved for inclusion in a web page (`iframe` is recommended then).\n",
+    "\n",
+    "You can also display it directly inside a notebook:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lab.show_html()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "21",
+   "metadata": {},
+   "source": [
+    "It's a bit empty... Let's add one moon."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "22",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lab.expand(target=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lab.show_html()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "24",
+   "metadata": {},
+   "source": [
+    "Few things about the generated graph:\n",
+    "\n",
+    "- Singletons (authors with no co-publications) are discarded by default.\n",
+    "- Authors are represented with their initials unless some picture url is provided (implicitly or explictly).\n",
+    "- You can hover an author to get her name. If you click, you have a modal with the list of publications.\n",
+    "- The width and length of an edge depend on the number of co-publications. If you click you have a modal with the list of co-publications."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "25",
+   "metadata": {},
+   "source": [
+    "## Make your own lab"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "26",
+   "metadata": {},
+   "source": [
+    "The easiest way to manage a lab is to specify an internal method `_author_iterator` that returns Lab authors. \n",
+    "\n",
+    "To GISMAP a lab, you just need to specify that method. Most of the time, this is done by scrapping some Web page(s). See the references for examples.\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "27",
+   "metadata": {},
+   "source": [
+    "## Example"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "28",
+   "metadata": {},
+   "source": [
+    "The `LaasLab` class automatically builds a lab representation from `https://www.laas.fr/fr/equipes/*team_name*/`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gismap.lab import Solace\n",
+    "solace = Solace()\n",
+    "solace.update_authors()\n",
+    "solace.update_publis()\n",
+    "solace.expand(target=10)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "30",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "solace.show_html()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{gismap-0.1.0 → gismap-0.2.0}/gismap/__init__.py

@@ -2,6 +2,8 @@
 
 from importlib.metadata import metadata
 
+from gismap.sources.hal import HAL as HAL, HALAuthor as HALAuthor
+from gismap.sources.dblp import DBLP as DBLP, DBLPAuthor as DBLPAuthor
 from gismap.utils.common import get_classes as get_classes
 from gismap.gismo import make_gismo as make_gismo
 from gismap.search import (