Merge pull request #540 from pretendWhale/release_v2.5.0

Release v2.5.0
MarkUsProject · Aug 19, 2024 · f2012fd · f2012fd
2 parents 13f2b63 + d2003e6
commit f2012fd
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,9 +1,9 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.8.0
     hooks:
     - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
     - id: flake8
diff --git a/Changelog.md b/Changelog.md
@@ -1,6 +1,13 @@
 # CHANGELOG
 All notable changes to this project will be documented here.
 
+## [v2.5.0]
+- Ensure R packages are correctly installed (#535)
+- Make PyTA version a setting (#536)
+- Add `libxml2-dev` to server `Dockerfile`, required by R `tidyverse` library (#539)
+- Display stderr contents if R packages fail to install (#539)
+- Do not display `testthat` failure messages when test case passes (#539)
+
 ## [v2.4.4]
 - Add tidyverse as a default R tester package (#512)
 - For the Haskell tester, make stack resolver a test setting (#526)

diff --git a/client/requirements.txt b/client/requirements.txt
@@ -1,10 +1,10 @@
 flask==2.2.5;python_version<"3.8"
-flask==2.3.3;python_version>="3.8"
+flask==3.0.3;python_version>="3.8"
 python-dotenv==0.21.1;python_version<"3.8"
-python-dotenv==1.0.0;python_version>="3.8"
-rq==1.15.1
-redis==5.0.1
+python-dotenv==1.0.1;python_version>="3.8"
+rq==1.16.2
+redis==5.0.4
 jsonschema==4.17.3;python_version<"3.8"
-jsonschema==4.20.0;python_version>="3.8"
+jsonschema==4.22.0;python_version>="3.8"
 Werkzeug==2.2.3;python_version<"3.8"
-Werkzeug==2.3.8;python_version>="3.8"
+Werkzeug==3.0.3;python_version>="3.8"
diff --git a/server/.dockerfiles/Dockerfile b/server/.dockerfiles/Dockerfile
@@ -34,6 +34,7 @@ RUN apt-get update -y && \
                        libjpeg-dev \
                        libharfbuzz-dev \
                        libfribidi-dev \
+                       libxml2-dev \
                        r-base
 
 RUN useradd -ms /bin/bash $LOGIN_USER && \

diff --git a/server/autotest_server/__init__.py b/server/autotest_server/__init__.py
@@ -405,7 +405,10 @@ def update_test_settings(user, settings_id, test_settings, file_url):
             try:
                 tester_settings["_env"] = tester_install.create_environment(tester_settings, env_dir, default_env)
             except Exception as e:
-                raise Exception(f"create tester environment failed:\n{e}") from e
+                error_message = f"create tester environment failed:\n{e}"
+                if e.stderr:
+                    error_message += f"\nDetails (captured stderr):\n{e.stderr}"
+                raise Exception(error_message) from e
             test_settings["testers"][i] = tester_settings
         test_settings["_files"] = files_dir
         test_settings.pop("_error", None)

diff --git a/server/autotest_server/testers/pyta/requirements.txt b/server/autotest_server/testers/pyta/requirements.txt
@@ -1,3 +1 @@
-python-ta==1.4.2;python_version<"3.8"
-python-ta==2.7.0; python_version>="3.8"
 isort<5;python_version<"3.8"
diff --git a/server/autotest_server/testers/pyta/settings_schema.json b/server/autotest_server/testers/pyta/settings_schema.json
@@ -25,6 +25,11 @@
         "pip_requirements": {
           "title": "Package requirements",
           "type": "string"
+        },
+        "pyta_version": {
+          "title": "PyTA version",
+          "type": "string",
+          "default": null
         }
       }
     },

diff --git a/server/autotest_server/testers/pyta/setup.py b/server/autotest_server/testers/pyta/setup.py
@@ -3,15 +3,21 @@
 import json
 import subprocess
 
+PYTA_VERSION_PREFIX = "python-ta=="
+PYTA_VERSION = "2.7.0"
+
 
 def create_environment(settings_, env_dir, _default_env_dir):
     env_data = settings_.get("env_data", {})
     python_version = env_data.get("python_version", "3")
-    pip_requirements = ["wheel"] + env_data.get("pip_requirements", "").split()
+    env_properties = ["wheel"] + env_data.get("pip_requirements", "").split()
+    pyta_version = env_data.get("pyta_version", PYTA_VERSION)
+    pyta_version = PYTA_VERSION_PREFIX + pyta_version
+    env_properties.append(pyta_version)
     requirements = os.path.join(os.path.dirname(os.path.realpath(__file__)), "requirements.txt")
     pip = os.path.join(env_dir, "bin", "pip")
     subprocess.run([f"python{python_version}", "-m", "venv", "--clear", env_dir], check=True)
-    subprocess.run([pip, "install", "-r", requirements, *pip_requirements], check=True)
+    subprocess.run([pip, "install", "-r", requirements, *env_properties], check=True)
     return {"PYTHON": os.path.join(env_dir, "bin", "python3")}
 
 
@@ -22,6 +28,8 @@ def settings():
     python_versions = settings_["properties"]["env_data"]["properties"]["python_version"]
     python_versions["enum"] = py_versions
     python_versions["default"] = py_versions[-1]
+    pyta_version = settings_["properties"]["env_data"]["properties"]["pyta_version"]
+    pyta_version["default"] = PYTA_VERSION
     return settings_
 
 

diff --git a/server/autotest_server/testers/r/lib/r_tester_setup.R b/server/autotest_server/testers/r/lib/r_tester_setup.R
@@ -38,10 +38,13 @@ install_dep <- function(row) {
   } else {
     remote_type <- NA_character_
   }
+  if (!('stringi' %in% rownames(installed.packages))) {
+    install.packages(name, configure.args="--disable-pkg-config")
+  }
 
   # Check if package is already installed
   # TODO: make this work for remote packages (with '/' in the name)
-  if (name %in% installed.packages() &&
+  if (name %in% rownames(installed.packages()) &&
       (is.na(version) || version_satisfies_criterion(name, compare, version))) {
       print(paste("Skipping '", name, "': package already installed", sep=""))
       return()
@@ -61,7 +64,7 @@ install_dep <- function(row) {
     }
   }
 
-  if (!(name %in% installed.packages())) {
+  if (!(name %in% rownames(installed.packages()))) {
     stop("ERROR: Could not install package ", name)
   }
 }

diff --git a/server/autotest_server/testers/r/r_tester.py b/server/autotest_server/testers/r/r_tester.py
@@ -34,7 +34,10 @@ def run(self):
         successes = 0
         error = False
         for result in self.result:
-            messages.append(result["message"])
+            # Only add message if not a success, as testthat reports failure messages only
+            if result["type"] != "expectation_success":
+                messages.append(result["message"])
+
             if result["type"] == "expectation_success":
                 self.points_total += 1
                 successes += 1

diff --git a/server/autotest_server/testers/r/setup.py b/server/autotest_server/testers/r/setup.py
@@ -10,7 +10,13 @@ def create_environment(settings_, env_dir, default_env_dir):
     env = {"R_LIBS_SITE": env_dir, "R_LIBS_USER": env_dir}
 
     r_tester_setup = os.path.join(os.path.dirname(os.path.realpath(__file__)), "lib", "r_tester_setup.R")
-    subprocess.run(["Rscript", r_tester_setup, req_string], env={**os.environ, **env}, check=True)
+    subprocess.run(
+        ["Rscript", r_tester_setup, req_string],
+        env={**os.environ, **env},
+        check=True,
+        text=True,
+        capture_output=True,
+    )
 
     return {**env, "PYTHON": os.path.join(default_env_dir, "bin", "python3")}
 

diff --git a/server/requirements.txt b/server/requirements.txt
@@ -1,9 +1,10 @@
-rq==1.15.1
+rq==1.16.2
 click==8.1.7
-redis==5.0.1
+redis==5.0.4
 pyyaml==6.0.1
 jsonschema==4.17.3;python_version<"3.8"
-jsonschema==4.20.0;python_version>="3.8"
-requests==2.31.0
+jsonschema==4.22.0;python_version>="3.8"
+requests==2.31.0;python_version<"3.8"
+requests==2.32.3;python_version>="3.8"
 psycopg2-binary==2.9.9
 supervisor==4.2.5