gismap 0.2.1__tar.gz → 0.2.2__tar.gz

{gismap-0.2.1 → gismap-0.2.2}/HISTORY.md

@@ -7,6 +7,13 @@
   - Colors and size
   - Groups
 
+## 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).
@@ -16,7 +23,7 @@
 ## 0.2.0 (2025-08-31): EgoMaps!
 
 - New lab structure: EgoMap shows the people that revolves around you!
-- New lab method: expansion, which adds *moons* (neighbor reasearchers).
+- New lab method: expansion, which adds *moons* (neighbor researchers).
 - Add filters when building authors and publications.
 - Physic engine changed fo better visualization.
 - Multi-source handling fine-tuned.

{gismap-0.2.1 → gismap-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gismap
-Version: 0.2.1
+Version: 0.2.2
 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

{gismap-0.2.1 → gismap-0.2.2}/docs/conf.py

@@ -46,10 +46,9 @@ extensions = [
 ]
 
 # Remote NB execution
-nbsphinx_execute = 'always'
-nbsphinx_execute_arguments = [
-    "--InlineBackend.figure_formats={'svg', 'pdf'}"
-]
+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")

{gismap-0.2.1 → gismap-0.2.2}/docs/reference/lab.md

@@ -1,45 +1,70 @@
 # Laboratory
 
-Management of a group of people and their publications is made with the {class}`~gismap.lab.lab.Lab` abstract class.
+Management of a group of people and their publications is made with the {class}`~gismap.lab.labmap.LabMap` abstract class.
 
+## LabMaps
 
 ```{eval-rst}
-.. automodule:: gismap.lab.lab
+.. automodule:: gismap.lab.labmap
     :members:
 ```
 
-## Collaboration graph
+## EgoMaps
 
 ```{eval-rst}
-.. automodule:: gismap.lab.graph
+.. automodule:: gismap.lab.egomap
     :members:
 ```
 
+## Lab library
 
-## LIP6
+### LIP6
 
 ```{eval-rst}
 .. automodule:: gismap.lab.lip6
     :members:
 ```
 
-## Toulouse
+### Toulouse
 
 ```{eval-rst}
 .. automodule:: gismap.lab.toulouse
     :members:
 ```
 
-## Vis
+## Utilities
+
+### Lab author
+
+```{eval-rst}
+.. automodule:: gismap.lab.lab_author
+    :members:
+```
+
+### Graphs
+
+```{eval-rst}
+.. automodule:: gismap.lab.graph
+    :members:
+```
+
+### VisJS interface
 
 ```{eval-rst}
 .. automodule:: gismap.lab.vis
     :members:
 ```
 
-## Expansion
+### Expansion
 
 ```{eval-rst}
 .. automodule:: gismap.lab.expansion
     :members:
 ```
+
+### Filters
+
+```{eval-rst}
+.. automodule:: gismap.lab.filters
+    :members:
+```

{gismap-0.2.1 → gismap-0.2.2}/docs/reference/utils.md

@@ -22,7 +22,7 @@ Functions related to the `requests`.
 
 ## Logger
 
-Keep track of things that go wrong.
+Keep track of things.
 
 ```{eval-rst}
 .. automodule:: gismap.utils.logger

{gismap-0.2.1 → gismap-0.2.2}/docs/tutorials/egomap.ipynb

@@ -13,15 +13,15 @@
    "id": "1",
    "metadata": {},
    "source": [
-    "Every researcher is the center of her own universe. With EgoMaps, everyone can visualize that universe!\n",
+    "Every researcher is the center of his/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 *star*, 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."
+    "By default, EgoMaps comprise up to 50 researchers, selecting first planets (sorted by number of collaborations), then moons (sorted by connectivity)."
    ]
   },
   {
@@ -29,7 +29,7 @@
    "id": "2",
    "metadata": {},
    "source": [
-    "## Simple case"
+    "## Disclaimer"
    ]
   },
   {
@@ -37,19 +37,17 @@
    "id": "3",
    "metadata": {},
    "source": [
-    "For basic scenarios, you just need to enter the name of the researcher. For example:"
+    "**EgoMaps provide an engaging visualization of a researcher's egosystem.** In essence, they offer an intuitive way to explore and identify the research community or communities surrounding a given individual. By highlighting connections and relationships within a research network, EgoMaps aim to facilitate a deeper understanding of collaborative and thematic clusters in a researcher’s environment.\n",
+    "\n",
+    "It is important to emphasize that **EgoMaps are not designed nor intended to support any form of quantitative evaluation or ranking of researchers' work or impact.** Any such interpretation or usage is strongly discouraged, as the feature's primary purpose is to assist with qualitative exploration and visualization of research communities, not research assessment."
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "id": "4",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "from gismap.lab import EgoMap as Map\n",
-    "celine = Map(\"Céline Comte\")\n",
-    "celine.build()"
+    "## Simple case"
    ]
   },
   {
@@ -57,7 +55,7 @@
    "id": "5",
    "metadata": {},
    "source": [
-    "You can display your EgoMap with `show_html` and save it with `save_html`"
+    "For basic scenarios, you just need to enter the name of the researcher. For example:"
    ]
   },
   {
@@ -67,7 +65,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "celine.show_html()"
+    "from gismap.lab import EgoMap as Map\n",
+    "\n",
+    "celine = Map(\"Céline Comte\")\n",
+    "celine.build()"
    ]
   },
   {
@@ -75,122 +76,95 @@
    "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)"
+    "You can display your EgoMap with `show_html` and save it with `save_html`"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
-    "fabien.show_html()"
+    "celine.show_html()"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "9",
    "metadata": {},
    "source": [
-    "## Using specific DBs"
+    "## Adjusting the size"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "12",
+   "id": "10",
    "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."
+    "Depending on your degree, you may want to adjust the size of your universe with `target`. You can also personalize the *star* with a picture."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "11",
    "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)"
+    "nidhi = Map(\"Nidhi Hegde\")\n",
+    "nidhi.star.metadata.img = \"https://sites.ualberta.ca/~nidhih/images/circle1.png\"\n",
+    "nidhi.build(target=70)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
-    "mathilde.show_html()"
+    "nidhi.show_html()"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "13",
    "metadata": {},
    "source": [
-    "## Filtering"
+    "## Using specific DBs"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "16",
+   "id": "14",
    "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."
+    "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": "17",
+   "id": "15",
    "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)"
+    "mathilde = Map(\"Mathilde Labbé\", dbs=\"hal\")\n",
+    "mathilde.star.metadata.img = (\n",
+    "    \"https://0.academia-photos.com/282997/7894577/15068468/s200_mathilde.labbe.jpg\"\n",
+    ")\n",
+    "mathilde.build(target=25)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
-    "fanfan.show_html()"
+    "mathilde.show_html()"
    ]
   }
  ],

{gismap-0.2.1 → gismap-0.2.2}/docs/tutorials/lab_tutorial.ipynb

@@ -32,6 +32,7 @@
    "outputs": [],
    "source": [
     "from gismap.lab import LabAuthor\n",
+    "\n",
     "maria = LabAuthor(\"Maria Potop\")\n",
     "maria.auto_sources()"
    ]
@@ -59,7 +60,7 @@
    "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."
+    "This is actually: 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."
    ]
   },
   {
@@ -88,6 +89,7 @@
    "outputs": [],
    "source": [
     "from gismap.sources.hal import HAL\n",
+    "\n",
     "celine = LabAuthor(\"Céline Comte\")\n",
     "celine.auto_sources(dbs=[HAL])\n",
     "celine.sources"
@@ -132,13 +134,13 @@
    "id": "14",
    "metadata": {},
    "source": [
-    "In GISMAP, a Lab is a class whose instances have three methods:\n",
+    "In GISMAP, a LabMap 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."
+    "The simplest usable subclass of Lab is `ListMap`, which uses a list of names. For example, consider the executive committee of the LINCS."
    ]
   },
   {
@@ -148,8 +150,18 @@
    "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",
+    "from gismap.lab import ListMap\n",
+    "\n",
+    "lab = ListMap(\n",
+    "    author_list=[\n",
+    "        \"Tixeuil Sébastien\",\n",
+    "        \"Kofman Daniel\",\n",
+    "        \"Baccelli François\",\n",
+    "        \"Noirie Ludovic\",\n",
+    "        \"Bassi Francesca\",\n",
+    "    ],\n",
+    "    name=\"toy_example\",\n",
+    ")\n",
     "lab.update_authors()\n",
     "lab.authors"
    ]
@@ -170,7 +182,7 @@
    "id": "17",
    "metadata": {},
    "source": [
-    "Labs can be saved to you don't have to re-update them all the time."
+    "Maps can be saved to you don't have to re-update them all the time."
    ]
   },
   {
@@ -188,7 +200,7 @@
    "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",
+    "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 (e.g. with `iframe`).\n",
     "\n",
     "You can also display it directly inside a notebook:"
    ]
@@ -238,7 +250,7 @@
    "source": [
     "Few things about the generated graph:\n",
     "\n",
-    "- Singletons (authors with no co-publications) are discarded by default.\n",
+    "- Singletons (authors with no co-publications with the other nodes) are kept 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."
@@ -249,7 +261,7 @@
    "id": "25",
    "metadata": {},
    "source": [
-    "## Make your own lab"
+    "## Make your own LabMap"
    ]
   },
   {
@@ -257,9 +269,11 @@
    "id": "26",
    "metadata": {},
    "source": [
-    "The easiest way to manage a lab is to specify an internal method `_author_iterator` that returns Lab authors. \n",
+    "Gismap is intended to make easy the creation of LabMaps in many contexts.\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"
+    "The easiest way to manage a lab, apart from using ListMaps as shown above, is to specify an internal method `_author_iterator` that returns Lab authors. When it's done, you can create/refresh LabMaps as you see fit.\n",
+    "\n",
+    "How the iterator works is 100% up to you. Most of the time, this is done by scrapping some Web page(s) (see the references for examples), but many other options exist, e.g. read authors from a file, from a LDAP..."
    ]
   },
   {
@@ -275,7 +289,7 @@
    "id": "28",
    "metadata": {},
    "source": [
-    "The `LaasLab` class automatically builds a lab representation from `https://www.laas.fr/fr/equipes/*team_name*/`"
+    "The `Solace` class automatically builds a LabMap based on https://solace.cnrs.fr/people.html"
    ]
   },
   {
@@ -286,10 +300,11 @@
    "outputs": [],
    "source": [
     "from gismap.lab import Solace\n",
+    "\n",
     "solace = Solace()\n",
     "solace.update_authors()\n",
     "solace.update_publis()\n",
-    "solace.expand(target=10)"
+    "solace.expand()"
    ]
   },
   {

{gismap-0.2.1 → gismap-0.2.2}/gismap/gismo.py

@@ -11,7 +11,7 @@ def make_post_publi(lab):
 
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Lab that contains the corpus publications.
 
     Returns
@@ -32,7 +32,7 @@ def make_gismo(lab, vectorizer_parameters=None):
 
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Lab that contains publications.
     vectorizer_parameters: :class:`dict`
         Overriding parameters for the Countvectorizer of the gismo.

{gismap-0.2.1 → gismap-0.2.2}/gismap/lab/__init__.py

@@ -1,9 +1,9 @@
-from gismap.lab.lab import (
-    Lab as Lab,
-    ListLab as ListLab,
+from gismap.lab.labmap import (
+    LabMap as Map,
+    ListMap as ListMap,
 )
-from gismap.lab.lip6 import Lip6 as Lip6, Lip6Lab as Lip6Lab
-from gismap.lab.toulouse import Solace as Solace, LaasLab as LaasLab
+from gismap.lab.lip6 import Lip6Full as Lip6Full, Lip6Map as Lip6
+from gismap.lab.toulouse import SolaceMap as Solace, LaasMap as Laas
 from gismap.lab.graph import lab2graph as lab2graph
 from gismap.lab.vis import generate_html as generate_html
 from gismap.lab.egomap import EgoMap as EgoMap

{gismap-0.2.1 → gismap-0.2.2}/gismap/lab/egomap.py

@@ -1,12 +1,12 @@
-from gismap.lab.lab import Lab
+from gismap.lab.labmap import LabMap
 from gismap.lab.lab_author import LabAuthor
 
 
-class EgoMap(Lab):
+class EgoMap(LabMap):
     """
     Parameters
     ----------
-    sun
+    star
     args
     kwargs
 
@@ -20,21 +20,21 @@ class EgoMap(Lab):
     'Siu-Wai Ho', 'Sébastien Tixeuil', 'The-Dang Huynh', 'Yannick Carlinet']
     """
 
-    def __init__(self, sun, *args, **kwargs):
-        if isinstance(sun, str):
-            sun = LabAuthor(sun)
-        sun.metadata.position = (0, 0)
-        self.sun = sun
+    def __init__(self, star, *args, **kwargs):
+        if isinstance(star, str):
+            star = LabAuthor(star)
+        star.metadata.position = (0, 0)
+        self.star = star
         super().__init__(*args, **kwargs)
 
     def _author_iterator(self):
-        yield self.sun
+        yield self.star
 
     def build(self, **kwargs):
         target = kwargs.pop("target", 50)
         group = kwargs.pop("group", "moon")
-        self.update_authors(desc="Sun metadata")
-        self.update_publis(desc="Sun publications")
+        self.update_authors(desc="Star metadata")
+        self.update_publis(desc="Star publications")
         kwargs["target"] = target - len(self.authors)
         self.expand(group=None, desc="Planets", **kwargs)
         kwargs.update({"target": target - len(self.authors), "group": group})

{gismap-0.2.1 → gismap-0.2.2}/gismap/lab/expansion.py

@@ -53,7 +53,7 @@ def count_prospect_entries(lab):
 
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Reference lab.
 
     Returns
@@ -117,7 +117,7 @@ def get_prospects(lab):
     """
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Reference lab.
 
     Returns
@@ -150,7 +150,7 @@ def get_member_names(lab):
     """
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Reference lab.
 
     Returns