Merge branch 'master' into bugfix/truncate-debug-output

ersilia/auth/auth.py

@@ -6,7 +6,7 @@
 try:
     from github import Github
     from github.GithubException import UnknownObjectException
-except ModuleNotFoundError:
+except (ModuleNotFoundError, ImportError):
     Github = None
     UnknownObjectException = None
 

ersilia/cli/commands/test.py

@@ -20,11 +20,14 @@ def test_cmd():
     --------
     .. code-block:: console
 
-        With default settings:
-        $ ersilia test my_model -d /path/to/model
+        With basic testing:/
+        $ ersilia test eosxxxx --from_dir /path/to/model
 
-        With deep testing level and inspect:
-        $ ersilia test my_model -d /path/to/model --level deep --inspect --remote
+        With different sources to fetch the model:
+        $ ersilia test eosxxxx --from_github/--from_dockerhub/--from_s3
+
+        With different levels of testing:
+        $ ersilia test eosxxxx --shallow --from_github/--from_dockerhub/--from_s3
     """
 
     @ersilia_cli.command(
@@ -38,48 +41,79 @@ def test_cmd():
         "-l",
         "--level",
         "level",
-        help="Level of testing, None: for default, deep: for deep testing",
+        help="Level of testing, None: for default, deep: for deep testing, shallow: for shallow testing",
         required=False,
         default=None,
         type=click.STRING,
     )
     @click.option(
-        "-d",
-        "--dir",
-        "dir",
-        help="Model directory",
-        required=False,
+        "--from_dir",
+        default=None,
+        type=click.STRING,
+        help="Local path where the model is stored",
+    )
+    @click.option(
+        "--from_github",
+        is_flag=True,
+        default=False,
+        help="Fetch fetch directly from GitHub",
+    )
+    @click.option(
+        "--from_dockerhub",
+        is_flag=True,
+        default=False,
+        help="Force fetch from DockerHub",
+    )
+    @click.option(
+        "--from_s3", is_flag=True, default=False, help="Force fetch from AWS S3 bucket"
+    )
+    @click.option(
+        "--version",
         default=None,
         type=click.STRING,
+        help="Version of the model to fetch, when fetching a model from DockerHub",
     )
     @click.option(
-        "--inspect",
-        help="Inspect the model: More on the docs",
+        "--shallow",
         is_flag=True,
         default=False,
+        help="This flag is used to check shallow checks (such as container size, output consistency..)",
     )
     @click.option(
-        "--remote",
-        help="Test the model from remote git repository",
+        "--deep",
         is_flag=True,
         default=False,
+        help="This flag is used to check deep checks (such as computational performance checks)",
     )
     @click.option(
-        "--remove",
-        help="Remove the model directory after testing",
+        "--as_json",
         is_flag=True,
         default=False,
+        help="This flag is used to save the report as json file)",
     )
-    def test(model, level, dir, inspect, remote, remove):
+    def test(
+        model,
+        level,
+        from_dir,
+        from_github,
+        from_dockerhub,
+        from_s3,
+        version,
+        shallow,
+        deep,
+        as_json,
+    ):
         mt = ModelTester(
-            model_id=model,
-            level=level,
-            dir=dir,
-            inspect=inspect,
-            remote=remote,
-            remove=remove,
+            model,
+            level,
+            from_dir,
+            from_github,
+            from_dockerhub,
+            from_s3,
+            version,
+            shallow,
+            deep,
+            as_json,
         )
-        echo("Setting up model tester...")
-        mt.setup()
-        echo("Testing model...")
-        mt.run(output_file=None)
+        echo(f"Model testing started for: {model}")
+        mt.run()

ersilia/default.py

@@ -7,6 +7,7 @@
 
 # EOS environmental variables
 EOS = os.path.join(str(Path.home()), "eos")
+EOS_TMP = os.path.join(EOS, "temp")
 if not os.path.exists(EOS):
     os.makedirs(EOS)
 ROOT = os.path.dirname(os.path.realpath(__file__))

ersilia/publish/inspect.py

@@ -1,4 +1,5 @@
 import os
+import re
 import subprocess
 import time
 from collections import namedtuple
@@ -387,23 +388,42 @@ def validate_repo_structure(self):
 
     def _validate_dockerfile(self, dockerfile_content):
         lines, errors = dockerfile_content.splitlines(), []
-        for line in lines:
-            if line.startswith("RUN pip install"):
-                cmd = line.split("RUN ")[-1]
-                result = subprocess.run(
-                    cmd,
-                    shell=True,
-                    stdout=subprocess.PIPE,
-                    stderr=subprocess.PIPE,
-                    text=True,
-                )
-                if result.returncode != 0:
-                    errors.append(f"Failed to run {cmd}: {result.stderr.strip()}")
 
         if "WORKDIR /repo" not in dockerfile_content:
             errors.append("Missing 'WORKDIR /repo'.")
         if "COPY . /repo" not in dockerfile_content:
             errors.append("Missing 'COPY . /repo'.")
+
+        pip_install_pattern = re.compile(r"pip install (.+)")
+        version_pin_pattern = re.compile(r"^[a-zA-Z0-9_\-\.]+==[a-zA-Z0-9_\-\.]+$")
+
+        for line in lines:
+            line = line.strip()
+
+            match = pip_install_pattern.search(line)
+            if match:
+                packages_and_options = match.group(1).split()
+                skip_next = False
+
+                for item in packages_and_options:
+                    if skip_next:
+                        skip_next = False
+                        continue
+
+                    if item.startswith("--index-url") or item.startswith(
+                        "--extra-index-url"
+                    ):
+                        skip_next = True
+                        continue
+
+                    if item.startswith("git+"):
+                        continue
+
+                    if not version_pin_pattern.match(item):
+                        errors.append(
+                            f"Package '{item}' in line '{line}' is not version-pinned (e.g., 'package==1.0.0')."
+                        )
+
         return errors
 
     def _validate_yml(self, yml_content):
@@ -417,18 +437,48 @@ def _validate_yml(self, yml_content):
         if not python_version:
             errors.append("Missing Python version in install.yml.")
 
+        version_pin_pattern = re.compile(r"^[a-zA-Z0-9_\-\.]+==[a-zA-Z0-9_\-\.]+$")
+
         commands = yml_data.get("commands", [])
         for command in commands:
-            if not isinstance(command, list) or command[0] != "pip":
+            if not isinstance(command, list) or len(command) < 2:
                 errors.append(f"Invalid command format: {command}")
                 continue
-            # package: name & version
-            name = command[1] if len(command) > 1 else None
+
+            tool = command[0]
+            _ = command[1]
             version = command[2] if len(command) > 2 else None
-            if not name:
-                errors.append(f"Missing package name in command: {command}")
-            if name and version:
-                pass
+
+            if tool in ("pip", "conda"):
+                if tool == "pip":
+                    pip_args = command[1:]
+                    skip_next = False
+
+                    for item in pip_args:
+                        if skip_next:
+                            skip_next = False
+                            continue
+
+                        if item.startswith("--index-url") or item.startswith(
+                            "--extra-index-url"
+                        ):
+                            skip_next = True
+                            continue
+
+                        if item.startswith("git+"):
+                            continue
+
+                        if not version_pin_pattern.match(item):
+                            errors.append(
+                                f"Package '{item}' in command '{command}' is not version-pinned (e.g., 'package==1.0.0')."
+                            )
+
+                elif tool == "conda" and not version:
+                    errors.append(
+                        f"Package in command '{command}' does not have a valid pinned version "
+                        f"(should be in the format ['conda', 'package_name', 'x.y.z'])."
+                    )
+
         return errors
 
     def _run_performance_check(self, n):
@@ -445,5 +495,5 @@ def _run_performance_check(self, n):
             return Result(False, f"Error serving model: {process.stderr.strip()}")
         execution_time = time.time() - start_time
         return Result(
-            True, f"{n} predictions executed in {execution_time:.2f} seconds."
+            True, f"{n} predictions executed in {execution_time:.2f} seconds. \n"
         )