Merge pull request #14 from tuneinsight/release-v1.1.2

v1.1.2 release

Author: fhoussiau

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tuneinsight
-Version: 1.1.0
+Version: 1.1.2
 Summary: Official Python SDK for the Tune Insight API. The current version is compatible with the same version of the API.
 License: Apache-2.0
 Author: Tune Insight SA
@@ -10,22 +10,26 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Provides-Extra: full
 Requires-Dist: PyYAML (>=6.0,<7.0)
 Requires-Dist: attrs (>=21.3.0)
 Requires-Dist: black (==24.2.0)
 Requires-Dist: certifi (>=2024.07.04,<2025.0.0)
 Requires-Dist: cryptography (>=44.0.1,<45.0.0)
 Requires-Dist: h11 (>=0.16.0,<0.17.0)
 Requires-Dist: httpx (>=0.15.4,<0.28.0)
+Requires-Dist: ipython (==8.18.1)
 Requires-Dist: jinja2 (>=3.1.6,<4.0.0)
-Requires-Dist: jupyter (>=1.1.1,<2.0.0)
-Requires-Dist: jupyterlab (==4.2.5)
+Requires-Dist: jupyter (>=1.1.1,<2.0.0) ; extra == "full"
+Requires-Dist: jupyter-client (>=8.6.3,<9.0.0) ; extra == "full"
+Requires-Dist: jupyterlab (>=4.3.6,<5.0.0) ; extra == "full"
 Requires-Dist: matplotlib (>=3.5.0,<4.0.0)
-Requires-Dist: notebook (>=6.4.11,<7.0.0)
+Requires-Dist: notebook (>=7.3.3,<8.0.0) ; extra == "full"
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: python-dateutil (>=2.8.0,<3.0.0)
 Requires-Dist: python-dotenv (>=0.21.0,<0.22.0)
-Requires-Dist: python-keycloak (>=3.9.0,<4.0.0)
+Requires-Dist: python-keycloak
+Requires-Dist: tornado (>=6.5.0,<7.0.0) ; extra == "full"
 Requires-Dist: tqdm (>=4.66.4,<5.0.0)
 Requires-Dist: typing-extensions (>=4.6.3,<5.0.0)
 Description-Content-Type: text/markdown
@@ -56,6 +60,14 @@ Note that versions `0.13.1` and older are not available on `pip`: [contact us](t
 
 It is recommended to set up a custom environment for the SDK, e.g. using [`conda`](https://anaconda.org/anaconda/conda).
 
+### Installing optional dependencies
+
+Starting with version 1.1.1, some dependencies are no longer packaged with the SDK to make the installation lighter. These include all dependencies related to Jupyter notebooks. If size is not a constraint, you can install all dependencies by adding `[full]` to the package name:
+
+```bash
+pip install tuneinsight[full]
+```
+
 ### Testing your implementation
 
 After installing the package, run the following command in your terminal.
@@ -74,6 +86,14 @@ The Tune Insight SDK is correctly installed.
 
 Refer to the [troubleshooting](#troubleshooting) section if you see any ❌.
 
+Note: if you did not install the full package, you might see the following error message that can be safely ignored:
+
+```
+Checking optional packages:
+# Jupyter is available  ❌
+        Jupyter is not installed, use `pip install tuneinsight[full]` to install it if needed.
+```
+
 ### Connecting to a server
 
 To further test your implementation, you can open a Python interpreter (e.g. a Jupyter notebook), and run the following commands, replacing `api_url` and `frontend_client_id` with the appropriate values. This will open a browser window asking you to log in to your Tune Insight account.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tuneinsight"
-version = "1.1.0"
+version = "1.1.2"  # Ignored.
 description = "Official Python SDK for the Tune Insight API. The current version is compatible with the same version of the API."
 authors = ["Tune Insight SA"]
 license = "Apache-2.0"
@@ -21,35 +21,45 @@ format = "{base}"
 
 [tool.poetry.dependencies]
 python = ">3.9.0,<3.9.1 || >3.9.1,<4.0"
-python-keycloak = "^3.9.0"
+python-keycloak = "*"
 PyYAML = "^6.0"
-notebook = "^6.4.11"
 python-dotenv = "^0.21.0"
 python-dateutil = "^2.8.0"
 matplotlib = "^3.5.0"
 typing-extensions = "^4.6.3"
-h11 = "^0.16.0"
-jinja2 = "^3.1.6"
-cryptography = "^44.0.1"
+pandas = "^2.2.3"
+tqdm = "^4.66.4"
+ipython = "8.18.1"
+black = "24.2.0"
 
-# Required by ge_co_rest_api
+# Required by the REST API models.
 httpx = ">=0.15.4,<0.28.0"
 attrs = ">=21.3.0"
 certifi = "^2024.07.04"
-black = "24.2.0"
-tqdm = "^4.66.4"
+jinja2 = "^3.1.6"
 
-jupyter = "^1.1.1"
-pandas = "^2.2.3"
-jupyterlab = "4.2.5"
+# Minimal versions required to fix known vulnerabilities in imports.
+h11 = "^0.16.0"
+cryptography = "^44.0.1"
+
+# Extras for the "full" install (somewhat heavy packages).
+notebook = { version = "^7.3.3", optional = true}
+jupyter = { version = "^1.1.1", optional = true}
+jupyterlab = { version = "^4.3.6", optional = true}
+tornado = { version = "^6.5.0", optional = true}
+jupyter-client = { version = "^8.6.3", optional = true}
 
 [tool.poetry.group.dev.dependencies]
 selenium = "^4.9.1"
 wheel = "^0.38.1"
 docker = "^6.0.1"
-pylint = "^2.13.2"
+pylint = "^3.3.7"
 pyvcf3 = "^1.0.3" # For GWAS .vcf file parsing
 pytest = "^8.1.1"
+jsonschema = "^4.24.0"
+
+[tool.poetry.extras]
+full = ["notebook", "jupyter", "jupyterlab", "tornado", "jupyter-client"]
 
 [tool.poetry.scripts]
 test-ti-install = "tuneinsight.utils.test:test_install"

src/tuneinsight/api/api-checksum

@@ -1 +1 @@
-b023866fb4734796dcf385bd51e14abd8711a989ad73876a1fee8b49e2f3c775
+b023866fb4734796dcf385bd51e14abd8711a989ad73876a1fee8b49e2f3c775

src/tuneinsight/api/sdk/api/api_admin/get_config.py

@@ -28,11 +28,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy
 

src/tuneinsight/api/sdk/api/api_admin/get_settings.py

@@ -22,11 +22,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy
 

src/tuneinsight/api/sdk/api/api_admin/patch_settings.py

@@ -25,11 +25,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy
 

src/tuneinsight/api/sdk/api/api_admin/post_storage.py

@@ -25,11 +25,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy
 

src/tuneinsight/api/sdk/api/api_computations/compute.py

@@ -121,11 +121,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy
 

src/tuneinsight/api/sdk/api/api_computations/delete_comp_bookmark.py

@@ -21,11 +21,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy
 

src/tuneinsight/api/sdk/api/api_computations/delete_computation.py

@@ -22,11 +22,11 @@ def _get_kwargs(
     # Set the proxies if the client has proxies set.
     proxies = None
     if hasattr(client, "proxies") and client.proxies is not None:
-        https_proxy = client.proxies.get("https")
+        https_proxy = client.proxies.get("https://")
         if https_proxy:
             proxies = https_proxy
         else:
-            http_proxy = client.proxies.get("http")
+            http_proxy = client.proxies.get("http://")
             if http_proxy:
                 proxies = http_proxy