Merge branch 'drop-python3.7-support' of https://github.com/Darkbeast…

…-glitch/ersilia into drop-python3.7-support

ersilia/cli/cmd.py

@@ -14,9 +14,9 @@ def catalog(self):
         m = importlib.import_module("ersilia.cli.commands.catalog")
         m.catalog_cmd()
 
-    def clear(self):
-        m = importlib.import_module("ersilia.cli.commands.clear")
-        m.clear_cmd()
+    def uninstall(self):
+        m = importlib.import_module("ersilia.cli.commands.uninstall")
+        m.uninstall_cmd()
 
     def close(self):
         m = importlib.import_module("ersilia.cli.commands.close")

ersilia/cli/commands/catalog.py

@@ -30,7 +30,7 @@ def catalog_cmd():
         help="Show more information than just the EOS identifier",
     )
     @click.option(
-        "--card",
+      "--card",
         is_flag=True,
         default=False,
         help="Use this flag to display model card for a given model ID",
@@ -40,9 +40,15 @@ def catalog_cmd():
         type=click.STRING,
         required=False,
     )
+    @click.option(
+        "--as-table",
+        is_flag=True,
+        default=False,
+        help="Show catalog in table format",
+    )
     def catalog(
-        local=False, file_name=None, browser=False, more=False, card=False, model=None
-    ):
+        local=False, file_name=None, browser=False, more=False, card=False, model=None, as_table=False
+        ):
         if card and not model:
             click.echo(
                 click.style("Error: --card option requires a model ID", fg="red"),
@@ -80,6 +86,7 @@ def catalog(
             mc.airtable()
             return
         catalog_table = mc.local() if local else mc.hub()
+
         if local and not catalog_table.data:
             click.echo(
                 click.style(
@@ -89,7 +96,7 @@ def catalog(
             )
             return
         if file_name is None:
-            catalog = catalog_table.as_json()
+            catalog = catalog_table.as_table() if as_table else catalog_table.as_json()
         else:
             catalog_table.write(file_name)
             catalog = None

ersilia/cli/commands/uninstall.py

@@ -0,0 +1,15 @@
+from . import ersilia_cli
+from ...utils.uninstall import Uninstaller
+
+
+def uninstall_cmd():
+    """Uninstalls all Ersilia artifacts present locally on the user's system"""
+
+    # Example usage: ersilia setup
+    @ersilia_cli.command(
+        short_help="Uninstall ersilia",
+        help="Uninstalls all Ersilia artifacts present locally on the user's system.",
+    )
+    def uninstall():
+        ui = Uninstaller()
+        ui.uninstall()

ersilia/cli/create_cli.py

@@ -10,7 +10,7 @@ def create_ersilia_cli():
 
     cmd.auth()
     cmd.catalog()
-    cmd.clear()
+    cmd.uninstall()
     cmd.close()
     cmd.delete()
     cmd.example()

ersilia/default.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 import shutil
 import os
+from enum import Enum
 
 # EOS environmental variables
 EOS = os.path.join(str(Path.home()), "eos")
@@ -29,6 +30,7 @@
 DEFAULT_API_NAME = "run"
 PACKMODE_FILE = "pack_mode.txt"
 CARD_FILE = "card.json"
+UNPROCESSABLE_INPUT="UNPROCESSABLE_INPUT"
 DOTENV_FILE = ".env"
 API_SCHEMA_FILE = "api_schema.json"
 MODEL_SIZE_FILE = "size.json"
@@ -104,6 +106,22 @@
         os.path.join(ROOT, "utils", "supp", _resolve_script), resolve_script
     )
 
+# Catalog table border constants
+class TableConstants(str, Enum):
+    TOP_LEFT = "┌"
+    TOP_MIDDLE = "┬"
+    TOP_RIGHT = "┐"
+    HORIZONTAL = "─"
+    VERTICAL = "│"
+    MIDDLE_LEFT = "├"
+    MIDDLE_MIDDLE = "┼"
+    MIDDLE_RIGHT = "┤"
+    BOTTOM_LEFT = "└"
+    BOTTOM_MIDDLE = "┴"
+    BOTTOM_RIGHT = "┘"
+    CELL_PADDING = " "
+    COLUMN_SEPARATOR = " | "
+
 snippet = (
     """
 # >>> ersilia >>>

ersilia/hub/content/catalog.py

@@ -11,6 +11,7 @@
 from ...utils.identifiers.model import ModelIdentifier
 from ...auth.auth import Auth
 from ...default import GITHUB_ORG, BENTOML_PATH, MODEL_SOURCE_FILE
+from ...default import TableConstants
 from ... import logger
 
 try:
@@ -42,6 +43,122 @@ def as_json(self):
         R = self.as_list_of_dicts()
         return json.dumps(R, indent=4)
 
+    def generate_separator_line(self, left, middle, right, horizontal, widths):
+        """
+        Generates a separator line for the table based on the given borders and column widths.
+
+        The line starts with a 'left' border, followed by repeated 'horizontal' 
+        sections for each column's width, joined by 'middle' separators, and ends 
+        with a 'right' border.
+
+        Args:
+            left (str): The character to use for the left border of the line.
+            middle (str): The character to use between columns (as separators).
+            right (str): The character to use for the right border of the line.
+            horizontal (str): The character used to draw the horizontal border.
+            widths (list[int]): A list of column widths to determine how much 
+                                horizontal space each column takes.
+
+        Returns:
+            str: The formatted separator line as a string.
+        """
+        return left + middle.join(horizontal * (width + 2) for width in widths) + right
+
+    def as_table(self):
+        """
+        Returns the catalog data in table format. The method calculates the 
+        column widths dynamically by determining the maximum width of each column, 
+        based on the data and column headers.
+
+        A row format string is then constructed using the column widths, 
+        specifying that each cell is left-aligned and padded with a column seperator sperating the rows.
+
+        The method starts by constructing the top border using the 
+        'generate_separator_line' helper. It then adds the headers, 
+        formatted to fit the column widths, followed by a separator line
+        also created by the helper function.
+
+        A 'for' loop iterates over the data rows, adding each row to the 
+        table with borders and padding. After each row, a separator line is inserted. 
+        Finally, the bottom border is added using the helper function, completing the table.
+
+        """
+        column_widths = [
+            max(
+                len(str(item)) if item is not None else 0
+                for item in [col] + [row[i] for row in self.data]
+            )
+            for i, col in enumerate(self.columns)
+        ]
+
+        table_constants = TableConstants
+
+        row_format = table_constants.COLUMN_SEPARATOR.join(
+            f"{{:<{width}}}" for width in column_widths
+        )
+
+        table = (
+            self.generate_separator_line(
+                table_constants.TOP_LEFT,
+                table_constants.TOP_MIDDLE,
+                table_constants.TOP_RIGHT,
+                table_constants.HORIZONTAL,
+                column_widths,
+            )
+            + "\n"
+        )
+        table += (
+            table_constants.VERTICAL
+            + table_constants.CELL_PADDING
+            + row_format.format(*self.columns)
+            + table_constants.CELL_PADDING
+            + table_constants.VERTICAL
+            + "\n"
+        )
+        table += (
+            self.generate_separator_line(
+                table_constants.MIDDLE_LEFT,
+                table_constants.MIDDLE_MIDDLE,
+                table_constants.MIDDLE_RIGHT,
+                table_constants.HORIZONTAL,
+                column_widths,
+            )
+            + "\n"
+        )
+
+        for index, row in enumerate(self.data):
+            row = [str(item) if item is not None else "" for item in row]
+            table += (
+                table_constants.VERTICAL
+                + table_constants.CELL_PADDING
+                + row_format.format(*row)
+                + table_constants.CELL_PADDING
+                + table_constants.VERTICAL
+                + "\n"
+            )
+
+            if index < len(self.data) - 1:
+                table += (
+                    self.generate_separator_line(
+                        table_constants.MIDDLE_LEFT,
+                        table_constants.MIDDLE_MIDDLE,
+                        table_constants.MIDDLE_RIGHT,
+                        table_constants.HORIZONTAL,
+                        column_widths,
+                    )
+                    + "\n"
+                )
+
+        table += self.generate_separator_line(
+            table_constants.BOTTOM_LEFT,
+            table_constants.BOTTOM_MIDDLE,
+            table_constants.BOTTOM_RIGHT,
+            table_constants.HORIZONTAL,
+            column_widths,
+        )
+
+        return table
+
     def write(self, file_name):
         with open(file_name, "w") as f:
             if file_name.endswith(".csv"):
@@ -73,7 +190,7 @@ def _is_eos(self, s):
             if not self.mi.is_test(s):
                 return True
         return False
-    
+
     def _get_item(self, card, item):
         if "card" in card:
             card = card["card"]
@@ -100,15 +217,15 @@ def _get_input(self, card):
 
     def _get_output(self, card):
         return self._get_item(card, "output")[0]
-    
+
     def _get_model_source(self, model_id):
         model_source_file = os.path.join(self._model_path(model_id), MODEL_SOURCE_FILE)
         if os.path.exists(model_source_file):
             with open(model_source_file) as f:
                 return f.read().rstrip()
         else:
             return None
-        
+
     def _get_service_class(self, card):
         if "service_class" in card:
             return card["service_class"]
@@ -207,7 +324,18 @@ def local(self):
                 output = self._get_output(card)
                 model_source = self._get_model_source(model_id)
                 service_class = self._get_service_class(card)
-                R += [[model_id, slug, title, status, inputs, output, model_source, service_class]]
+                R += [
+                    [
+                        model_id,
+                        slug,
+                        title,
+                        status,
+                        inputs,
+                        output,
+                        model_source,
+                        service_class,
+                    ]
+                ]
             columns = [
                 "Identifier",
                 "Slug",

ersilia/io/types/compound.py

@@ -1,7 +1,6 @@
 import os
 import csv
 import random
-import importlib
 
 from ...utils.identifiers.arbitrary import ArbitraryIdentifier
 from ...setup.requirements.compound import (
@@ -12,6 +11,7 @@
 from ..shape import InputShapeSingle, InputShapeList, InputShapePairOfLists
 from .examples import compound as test_examples
 from . import EXAMPLES_FOLDER
+from ...utils.identifiers.compound import CompoundIdentifier
 
 
 EXAMPLES = "compound.tsv"
@@ -23,9 +23,7 @@ def __init__(self, input_shape):
         self.input_shape = input_shape
         self.example_file = os.path.join(EXAMPLES_FOLDER, EXAMPLES)
         self.setup()
-        self.identifier = importlib.import_module(
-            "ersilia.utils.identifiers.compound"
-        ).CompoundIdentifier()
+        self.identifier = CompoundIdentifier()
         self.arbitrary_identifier = ArbitraryIdentifier()
         if type(self.input_shape) is InputShapeSingle:
             self.logger.debug(

ersilia/setup/requirements/compound.py

@@ -11,7 +11,7 @@ def __init__(self):
             self.install()
 
     def install(self):
-        run_command("python -m pip install rdkit-pypi")
+        run_command("python -m pip install rdkit==2023.9.1")
 
 
 class ChemblWebResourceClientRequirement(object):