gismap 0.3.0__py3-none-any.whl → 0.4.1__py3-none-any.whl

gismap/sources/models.py

@@ -6,11 +6,43 @@ from gismap.utils.common import LazyRepr
 
 @dataclass(repr=False)
 class Author(LazyRepr):
+    """
+    Base class for authors in the database system.
+
+    Authors are identified primarily by their name and may have
+    database-specific subclasses with additional attributes like keys and aliases.
+
+    Parameters
+    ----------
+    name : :class:`str`
+        The author's name.
+    """
+
     name: str
 
 
 @dataclass(repr=False)
 class Publication(LazyRepr):
+    """
+    Base class for publications in the database system.
+
+    Publications contain metadata about academic papers including title,
+    authors, venue, type, and publication year.
+
+    Parameters
+    ----------
+    title : :class:`str`
+        The publication title.
+    authors : :class:`list`
+        List of :class:`Author` objects.
+    venue : :class:`str`
+        Publication venue (journal, conference, etc.).
+    type : :class:`str`
+        Publication type (e.g., 'journal', 'conference', 'book').
+    year : :class:`int`
+        Year of publication.
+    """
+
     title: str
     authors: list
     venue: str
@@ -20,18 +52,69 @@ class Publication(LazyRepr):
 
 @dataclass(repr=False)
 class DB(LazyRepr):
+    """
+    Abstract base class for database backends.
+
+    Provides the interface for searching authors and retrieving publications.
+    Subclasses must implement :meth:`search_author` and :meth:`from_author`.
+
+    Attributes
+    ----------
+    db_name : :class:`str`
+        Identifier for the database backend (e.g., 'hal', 'dblp', 'ldb').
+    """
+
     db_name: ClassVar[str] = None
 
     @classmethod
     def search_author(cls, name):
+        """
+        Search for authors matching the given name.
+
+        Parameters
+        ----------
+        name : :class:`str`
+            Name to search for.
+
+        Returns
+        -------
+        :class:`list`
+            List of matching :class:`Author` objects.
+        """
         raise NotImplementedError
 
     @classmethod
     def from_author(cls, a):
+        """
+        Retrieve publications for a given author.
+
+        Parameters
+        ----------
+        a : :class:`Author`
+            The author whose publications to retrieve.
+
+        Returns
+        -------
+        :class:`list`
+            List of :class:`Publication` objects.
+        """
         raise NotImplementedError
 
 
 def db_class_to_auth_class(db_class):
+    """
+    Find the Author subclass associated with a given DB class.
+
+    Parameters
+    ----------
+    db_class : :class:`type`
+        A DB subclass (e.g., HAL, DBLP, LDB).
+
+    Returns
+    -------
+    :class:`type` or None
+        The corresponding Author subclass, or None if not found.
+    """
     for subclass in Author.__subclasses__():
         if db_class in subclass.__mro__:
             return subclass

gismap/sources/multi.py

@@ -8,6 +8,22 @@ from gismap.utils.text import clean_aliases
 
 
 def score_author_source(dbauthor):
+    """
+    Compute a quality score for an author source.
+
+    Higher scores indicate more reliable author identification.
+    HAL idHal keys are preferred, followed by HAL pid, then DBLP/LDB.
+
+    Parameters
+    ----------
+    dbauthor: :class:`~gismap.sources.models.Author`
+        A database-specific author object.
+
+    Returns
+    -------
+    :class:`int`
+        Score value (higher is better).
+    """
     if dbauthor.db_name == "hal":
         if dbauthor.key_type == "fullname":
             return -1
@@ -15,18 +31,45 @@ def score_author_source(dbauthor):
             return 2
         else:
             return 3
-    elif dbauthor.db_name == "dblp":
+    elif dbauthor.db_name in ["dblp", "ldb"]:
         return 1
     else:
         return 0
 
 
 def sort_author_sources(sources):
+    """
+    Sort author sources by quality score in descending order.
+
+    Parameters
+    ----------
+    sources: :class:`list`
+        List of database-specific author objects.
+
+    Returns
+    -------
+    :class:`list`
+        Sorted list with highest-quality sources first.
+    """
     return sorted(sources, key=score_author_source, reverse=True)
 
 
 @dataclass(repr=False)
 class SourcedAuthor(Author):
+    """
+    An author aggregated from multiple database sources.
+
+    Combines author information from HAL, DBLP, and/or LDB into a single entity.
+    The primary source (first in the sorted list) determines the author's key.
+
+    Parameters
+    ----------
+    name: :class:`str`
+        The author's name.
+    sources: :class:`list`
+        List of database-specific author objects (HALAuthor, DBLPAuthor, LDBAuthor).
+    """
+
     sources: list = field(default_factory=list)
 
     @property
@@ -69,7 +112,7 @@ class SourcedAuthor(Author):
 
 
 publication_score_rosetta = {
-    "db_name": {"dblp": 1, "hal": 2},
+    "db_name": {"dblp": 1, "ldb": 1, "hal": 2},
     "venue": {"CoRR": -1, "unpublished": -2},
     "type": {"conference": 1, "journal": 2},
 }
@@ -89,6 +132,28 @@ def sort_publication_sources(sources):
 
 @dataclass(repr=False)
 class SourcedPublication(Publication):
+    """
+    A publication aggregated from multiple database sources.
+
+    Combines publication entries from HAL, DBLP, and/or LDB that refer
+    to the same paper. The primary source determines the publication's metadata.
+
+    Parameters
+    ----------
+    title: :class:`str`
+        Publication title.
+    authors: :class:`list`
+        List of author objects.
+    venue: :class:`str`
+        Publication venue.
+    type: :class:`str`
+        Publication type.
+    year: :class:`int`
+        Publication year.
+    sources: :class:`list`
+        List of database-specific publication objects.
+    """
+
     sources: list = field(default_factory=list)
 
     @property

gismap/utils/common.py

@@ -1,9 +1,14 @@
+from dataclasses import dataclass
+
 HIDDEN_KEYS = {"sources", "aliases", "abstract", "metadata"}
 
 
 class LazyRepr:
     """
-    MixIn that hides empty fields in dataclasses repr's.
+    MixIn that provides a clean repr for dataclasses.
+
+    Hides empty fields and fields in HIDDEN_KEYS from the repr string.
+    Private attributes (starting with '_') are also hidden.
     """
 
     def __repr__(self):
@@ -30,7 +35,7 @@ def unlist(x):
     return x[0] if (isinstance(x, list) and x) else x
 
 
-def get_classes(root, key="name"):
+def get_classes(root, key="name", recurse=False):
     """
     Parameters
     ----------
@@ -38,6 +43,8 @@ def get_classes(root, key="name"):
         Starting class (can be abstract).
     key: :class:`str`, default='name'
         Attribute to look-up
+    recurse: bool, default=False
+        Recursively traverse subclasses.
 
     Returns
     -------
@@ -50,13 +57,16 @@ def get_classes(root, key="name"):
     >>> from gismap.sources.models import DB
     >>> subclasses = get_classes(DB, key='db_name')
     >>> dict(sorted(subclasses.items())) # doctest: +NORMALIZE_WHITESPACE
-    {'dblp': <class 'gismap.sources.dblp.DBLP'>, 'hal': <class 'gismap.sources.hal.HAL'>}
+    {'dblp': <class 'gismap.sources.dblp.DBLP'>,
+    'hal': <class 'gismap.sources.hal.HAL'>,
+    'ldb': <class 'gismap.sources.ldb.LDB'>}
     """
     result = {
         getattr(c, key): c for c in root.__subclasses__() if getattr(c, key, None)
     }
-    for c in root.__subclasses__():
-        result.update(get_classes(c))
+    if recurse:
+        for c in root.__subclasses__():
+            result.update(get_classes(c, key=key, recurse=True))
     return result
 
 
@@ -83,23 +93,75 @@ def list_of_objects(clss, dico, default=None):
 
     >>> from gismap.sources.models import DB
     >>> subclasses = get_classes(DB, key='db_name')
-    >>> from gismap import HAL, DBLP
-    >>> list_of_objects([HAL, 'dblp'], subclasses)
-    [<class 'gismap.sources.hal.HAL'>, <class 'gismap.sources.dblp.DBLP'>]
+    >>> from gismap import HAL, DBLP, LDB
+    >>> list_of_objects([HAL, 'ldb'], subclasses)
+    [<class 'gismap.sources.hal.HAL'>, <class 'gismap.sources.ldb.LDB'>]
     >>> list_of_objects(None, subclasses, [DBLP])
     [<class 'gismap.sources.dblp.DBLP'>]
-    >>> list_of_objects(DBLP, subclasses)
-    [<class 'gismap.sources.dblp.DBLP'>]
+    >>> list_of_objects(LDB, subclasses)
+    [<class 'gismap.sources.ldb.LDB'>]
     >>> list_of_objects('hal', subclasses)
     [<class 'gismap.sources.hal.HAL'>]
     """
     if default is None:
         default = []
     if clss is None:
-        return default
+        return list_of_objects(clss=default, dico=dico)
     elif isinstance(clss, str):
         return [dico[clss]]
     elif isinstance(clss, list):
         return [cls for lcls in clss for cls in list_of_objects(lcls, dico, default)]
     else:
         return [clss]
+
+
+@dataclass(repr=False)
+class Data(LazyRepr):
+    """
+    Easy-going converter of dict to dataclass. Useful when you want to use attribute access
+    and do not care about giving a full description.
+
+    Examples
+    --------
+
+    >>> data = Data({
+    ... 'name': 'Alice',
+    ... 'age': 30,
+    ... 'address': {'street': '123 Main', 'city': 'Paris'},
+    ... 'hobbies': [{'name': 'jazz', 'level': 5}, {'name': 'code'}]})
+    >>> data # doctest: +NORMALIZE_WHITESPACE
+    Data(name='Alice', age=30, address=Data(street='123 Main', city='Paris'),
+    hobbies=[Data(name='jazz', level=5), Data(name='code')])
+    >>> data.hobbies[0].name
+    'jazz'
+    >>> data.todict()  # doctest: +NORMALIZE_WHITESPACE
+    {'name': 'Alice', 'age': 30, 'address': {'street': '123 Main', 'city': 'Paris'},
+    'hobbies': [{'name': 'jazz', 'level': 5}, {'name': 'code'}]}
+    """
+
+    def __init__(self, data):
+        self._wrap(data)
+
+    def _wrap(self, d):
+        for key, value in d.items():
+            wrapped = self._wrap_item(value)
+            setattr(self, key, wrapped)
+
+    def _wrap_item(self, item):
+        if isinstance(item, dict):
+            return Data(item)
+        elif isinstance(item, list):
+            return [self._wrap_item(subitem) for subitem in item]
+        return item
+
+    def todict(self):
+        res = {}
+        for key in self.__dict__:
+            value = getattr(self, key)
+            if hasattr(value, "todict"):
+                res[key] = value.todict()
+            elif isinstance(value, list):
+                res[key] = [v.todict() if hasattr(v, "todict") else v for v in value]
+            else:
+                res[key] = value
+        return res

gismap/utils/logger.py

@@ -2,3 +2,5 @@ import logging
 
 logger = logging.getLogger("GisMap")
 """Default logging interface."""
+
+logger.setLevel(logging.INFO)

gismap/utils/requests.py

@@ -21,7 +21,9 @@ def get(url, params=None, n_trials=10, verify=True):
         Entry point to fetch.
     params: :class:`dict`, optional
         Get arguments (appended to URL).
-    verify: :class:`bool`, optional
+    n_trials: :class:`int`, default=10
+        Number of attempts to fetch URL.
+    verify: :class:`bool`, default=True
         Verify certificates.
 
     Returns

gismap/utils/text.py

@@ -98,7 +98,7 @@ def asciify(text):
     """
     Parameters
     ----------
-    text::class:`str`
+    text: :class:`str`
         Some text (typically names) with annoying accents.
 
     Returns

gismap/utils/zlist.py

@@ -0,0 +1,88 @@
+from gismo.common import MixInIO
+import zstandard as zstd
+import numpy as np
+import pickle
+
+dctx = zstd.ZstdDecompressor()
+cctx = zstd.ZstdCompressor()
+
+
+class ZList(MixInIO):
+    """
+    Compressed list with frame-based storage.
+
+    Stores elements in compressed frames, allowing efficient memory usage
+    while maintaining random access. Uses zstandard compression.
+
+    Use as a context manager for building:
+
+        with ZList(frame_size=1000) as z:
+            for item in data:
+                z.append(item)
+
+    Parameters
+    ----------
+    frame_size : :class:`int`, default=1000
+        Number of elements per compressed frame.
+    """
+
+    def __init__(self, frame_size=1000):
+        self.frame_size = frame_size
+        self.frame = None
+        self._frame_index = None
+        self._blob = None
+        self._off = None
+        self._n = None
+        self._batch = None
+
+    def _merge_batch(self):
+        if self._batch:
+            frame = cctx.compress(pickle.dumps(self._batch))
+            self._blob += frame
+            self._off.append(len(self._blob))
+            self._batch = []
+
+    def append(self, entry):
+        """
+        Add an element to the list.
+
+        Parameters
+        ----------
+        entry
+            Element to add.
+        """
+        self._batch.append(entry)
+        self._n += 1
+        if len(self._batch) == self.frame_size:
+            self._merge_batch()
+
+    @property
+    def size(self):
+        return len(self._blob)
+
+    def __enter__(self):
+        self._blob = bytearray()
+        self._off = [0]
+        self._n = 0
+        self._batch = []
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self._merge_batch()
+        self._blob = bytes(self._blob)
+        self._off = np.array(self._off, dtype=int)
+
+    def load_frame(self, f):
+        self.frame = pickle.loads(
+            dctx.decompress(self._blob[self._off[f] : self._off[f + 1]])
+        )
+
+    def __getitem__(self, i):
+        g, f = i // self.frame_size, i % self.frame_size
+        if g != self._frame_index:
+            self.load_frame(g)
+            self._frame_index = g
+        return self.frame[f]
+
+    def __len__(self):
+        return self._n

{gismap-0.3.0.dist-info → gismap-0.4.1.dist-info}/METADATA

@@ -1,24 +1,26 @@
 Metadata-Version: 2.4
 Name: gismap
-Version: 0.3.0
-Summary: GisMap leverages DBLP and HAL databases to provide cartography tools for you and your lab.
+Version: 0.4.1
+Summary: GisMap: for researchers, by researchers. Research cartography tools leveraging DBLP and HAL.
 Project-URL: Repository, https://github.com/balouf/gismap
 Project-URL: Documentation, https://balouf.github.io/gismap
 Author-email: Fabien Mathieu <fabien.mathieu@normalesup.org>
 Maintainer-email: Fabien Mathieu <fabien.mathieu@normalesup.org>
 License-Expression: MIT
 License-File: AUTHORS.md
-Requires-Python: >=3.10
-Requires-Dist: bof>=0.3.5
+Requires-Python: <3.15,>=3.11
+Requires-Dist: beautifulsoup4>=4.14.3
+Requires-Dist: bof>=0.4.2
 Requires-Dist: distinctipy>=1.3.4
 Requires-Dist: domonic>=0.9.13
-Requires-Dist: gismo>=0.5.2
+Requires-Dist: gismo>=0.5.4
 Requires-Dist: ipykernel>=6.30.1
 Requires-Dist: ipywidgets>=8.1.8
+Requires-Dist: platformdirs>=4.5.1
 Requires-Dist: tqdm>=4.67.1
 Description-Content-Type: text/markdown
 
-# Generic Information Search: Mapping and Analysis of Publications
+# GisMap: for researchers, by researchers
 
 
 [![PyPI Status](https://img.shields.io/pypi/v/gismap.svg)](https://pypi.python.org/pypi/gismap)
@@ -28,7 +30,7 @@ Description-Content-Type: text/markdown
 [![License: MIT](https://img.shields.io/badge/license-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code Coverage](https://codecov.io/gh/balouf/gismap/branch/main/graphs/badge.svg)](https://codecov.io/gh/balouf/gismap/tree/main)
 
-GisMap leverages DBLP and HAL databases to provide cartography tools for you and your lab.
+GisMap (Generic Information Search: Mapping and Analysis of Publications) leverages DBLP and HAL databases to provide cartography tools for you and your lab.
 
 - Free software: MIT
 - Documentation: <https://balouf.github.io/gismap/>.
@@ -39,6 +41,7 @@ GisMap leverages DBLP and HAL databases to provide cartography tools for you and
 - Can be used by all researchers in Computer Science (DBLP endpoint) or based in France (HAL endpoint).
 - Aggregate publications from multiple databases, including multiple author keys inside the same database.
 - Automatically keeps track of a Lab/Department members and publications.
+- DBLP database can be used locally (LDB endpoint) to improve speed and reliability.
 - Builds interactive collaboration graphs.
 
 ## Test GisMap online!
@@ -52,6 +55,7 @@ For example:
 - [Tutorial: Making EgoMaps](https://mybinder.org/v2/gh/balouf/gismap/HEAD?urlpath=%2Fdoc%2Ftree%2Fdocs%2Ftutorials%2Fegomap.ipynb)
 - [Jupyter Lab instance with GisMap installed](https://mybinder.org/v2/gh/balouf/gismap/HEAD)
 
+**WARNING**: don't use LDB on `binder`, which does not provide enough memory yet. Only HAL and legacy DBLP work on binder.
 
 ## Quickstart
 
@@ -61,17 +65,28 @@ Install GisMap:
 $ pip install gismap
 ```
 
-Use GisMap to produce a collaboration graph (HTML):
+Use GisMap to display a collaboration graph (HTML) from a Notebook:
 
 ```pycon
->>> from gismap.sources.hal import HAL
->>> from gismap.lab import ListLab
->>> lab = ListLab(["Fabien Mathieu", "François Baccelli", "Ludovic Noirie", "Céline Comte", "Sébastien Tixeuil"], dbs="hal")
+>>> from gismap.lab import ListMap
+>>> lab = ListMap(["Fabien Mathieu", "François Baccelli", "Ludovic Noirie", "Céline Comte", "Sébastien Tixeuil"], dbs="hal")
 >>> lab.update_authors()
 >>> lab.update_publis()
 >>> lab.show_html()
 ```
 
+If you are not using Jupyter Lab/Notebook, rich display will not work.
+Instead, save the HTML and display it on your browser:
+
+```pycon
+>>> from gismap.lab import ListMap
+>>> lab = ListMap(["Fabien Mathieu", "François Baccelli", "Ludovic Noirie", "Céline Comte", "Sébastien Tixeuil"], dbs="hal")
+>>> lab.update_authors()
+>>> lab.update_publis()
+>>> lab.save_html("my_graph")
+```
+
+
 ## Credits
 
 This package was created with [Cookiecutter][CC] and the [Package Helper 3][PH3] project template.

gismap-0.4.1.dist-info/RECORD

@@ -0,0 +1,43 @@
+gismap/__init__.py,sha256=FHZLy3T2zFVrFRe3sqSRTuXkZ6DYise9HtXCWWfXrys,866
+gismap/author.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/build.py,sha256=lyJgrlvf2xXD4vfYn8VjwKloPBL4DKnplWQuwo2Sh8w,693
+gismap/gismap.py,sha256=h0hwdogXGFqerm-5ZPeT-irPn91pCcQRjiHThXsRzEk,19
+gismap/gismo.py,sha256=oDAryl4XQzHE0tUmOWC-3G1n_zUgTeykPL-JWSDYwe0,6307
+gismap/search.py,sha256=EQTts33P47WqbTBFNC0RwXXUJ0Teb6rJMru2gKRJP5k,6289
+gismap/gisgraphs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/gisgraphs/builder.py,sha256=GlyvKIfeUlkCD1Oap5qtY5dYBHTEQYT_YXnedt7IK44,3971
+gismap/gisgraphs/graph.py,sha256=hipfxQ_l5lfIyOkrQAb8oVMERIbe8fcFiz2gASbcNsQ,7320
+gismap/gisgraphs/groups.py,sha256=1E-7Xrv0uDw2SgqwtdjgeRLVBLaC7agUrrVics4jVLs,2405
+gismap/gisgraphs/js.py,sha256=Gbz5nMWORabZkgIdyZAe1sMlnwJZ9jy7sLrx0vYStzI,6283
+gismap/gisgraphs/options.py,sha256=lmUSnfSwrZQyJpGGs16JUGDIQNcJeX4Y0tA8cyC0nuM,817
+gismap/gisgraphs/style.py,sha256=sXNUnv690kxiJiRQZ7lv4iKKrsxMqAfblheJbqesd48,4653
+gismap/gisgraphs/widget.py,sha256=-wS98lHjewMYH6hEndAnb7MOe-mDOa9FVHeVUY0QRqY,5086
+gismap/lab/__init__.py,sha256=ifyZqI9BpC5NRlMfSmJ671tnKWJDoXbo18iDoE-VR1s,181
+gismap/lab/egomap.py,sha256=MFtuqvCHJCF6IG94uwHTdED1jwK6-BtQTLPfxk88GOQ,2071
+gismap/lab/expansion.py,sha256=dmOHbbd69EGPaQ0gpH1bRW5q59fbG5T_K0tl8E6QmDg,7393
+gismap/lab/filters.py,sha256=pG_g2POQXMbyUUw0aXOaeyiGBbiSc7M2NzxLCTQrALk,1875
+gismap/lab/lab_author.py,sha256=RQWeAmprs_h1_RS7slR0ApWXkuh8iekV5dHQgPSj-rY,5123
+gismap/lab/labmap.py,sha256=owvvDfOBNmyyp4K7lgmZAnF6gWl3SJTto1Qpr96Qu_c,6620
+gismap/lab_examples/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/lab_examples/cedric.py,sha256=nsRR_dcnTp9PIXKe3A0Is5beG4IIDPtspNP79BlkYNc,1906
+gismap/lab_examples/lamsade.py,sha256=SRv_kWN0WPKp0KEFwP7SmWRvKPCRMLG3ya_w9VIrjCM,1330
+gismap/lab_examples/lincs.py,sha256=-mIVMGQMrtCtJ3N-oCU8j4Ko9mDuhEPB_pA0gaIw4QA,1126
+gismap/lab_examples/lip6.py,sha256=K32Jqe3-o99QYI--akmwBDFAWKgq0HFEk_psC4akR60,1740
+gismap/lab_examples/toulouse.py,sha256=Zg6xZFxGfl3FvBh9R5hJSMRyC16DL7aJwLU9H_9mkSA,2139
+gismap/sources/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/sources/dblp.py,sha256=T6vLo4T7mB5IqHIl_Q7QTU2whkhzfR30H9ULjnLaNFw,5321
+gismap/sources/dblp_ttl.py,sha256=B-gHxBfP0zIWIYNMqLbKrOnbu9ybqByU8G4FNj0NChg,5597
+gismap/sources/hal.py,sha256=aHeX3C2al75NCMNKksTP2-4Jj6sAaI9iyKuL7F-V7UA,11278
+gismap/sources/ldb.py,sha256=ub7ctY82YahvkOvn8XYTG643cyi4gXfTpMspGMhT5dE,23570
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{gismap-0.3.0.dist-info → gismap-0.4.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

gismap-0.3.0.dist-info/RECORD

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