From 56413bd9fd8e52efc2fdd12a65e027bebe7616d8 Mon Sep 17 00:00:00 2001
From: faricazjj <faricazjj@gmail.com>
Date: Fri, 4 Sep 2026 09:15:34 -0400
Subject: [PATCH] Stop tracking IDE and local artifact outputs

Co-authored-by: Cursor <cursoragent@cursor.com>
---
 .gitignore                                    |  2 +
 .idea/.gitignore                              |  8 --
 .idea/.name                                   |  1 -
 .idea/Deep_Clustering_Survival_Machines.iml   | 19 ----
 .idea/deployment.xml                          | 57 ------------
 .idea/inspectionProfiles/Project_Default.xml  | 89 -------------------
 .../inspectionProfiles/profiles_settings.xml  |  6 --
 .idea/misc.xml                                |  4 -
 .idea/modules.xml                             |  8 --
 .idea/other.xml                               |  7 --
 .idea/remote-mappings.xml                     | 16 ----
 11 files changed, 2 insertions(+), 215 deletions(-)
 delete mode 100644 .idea/.gitignore
 delete mode 100644 .idea/.name
 delete mode 100644 .idea/Deep_Clustering_Survival_Machines.iml
 delete mode 100644 .idea/deployment.xml
 delete mode 100644 .idea/inspectionProfiles/Project_Default.xml
 delete mode 100644 .idea/inspectionProfiles/profiles_settings.xml
 delete mode 100644 .idea/misc.xml
 delete mode 100644 .idea/modules.xml
 delete mode 100644 .idea/other.xml
 delete mode 100644 .idea/remote-mappings.xml

diff --git a/.gitignore b/.gitignore
index 8c07805..39f80bf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,9 +15,11 @@ venv/
 tmp_*/
 *.log
 logs/**/*.log
+logs/
 results/*.db
 results/*.sqlite
 results/*_all_trials.csv
+results/
 
 # Large generated artifacts
 Figures/*.png
diff --git a/.idea/.gitignore b/.idea/.gitignore
deleted file mode 100644
index 35410ca..0000000
--- a/.idea/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-# 默认忽略的文件
-/shelf/
-/workspace.xml
-# 基于编辑器的 HTTP 客户端请求
-/httpRequests/
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
diff --git a/.idea/.name b/.idea/.name
deleted file mode 100644
index 6ad3729..0000000
--- a/.idea/.name
+++ /dev/null
@@ -1 +0,0 @@
-Deep_Clustering_Survival_Machines
\ No newline at end of file
diff --git a/.idea/Deep_Clustering_Survival_Machines.iml b/.idea/Deep_Clustering_Survival_Machines.iml
deleted file mode 100644
index 4529887..0000000
--- a/.idea/Deep_Clustering_Survival_Machines.iml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
-    <orderEntry type="jdk" jdkName="Remote Python 3.8.12 (sftp://houbo@exxact:22/home/houbo/.conda/envs/hobo/bin/python)" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="PyDocumentationSettings">
-    <option name="renderExternalDocumentation" value="true" />
-  </component>
-  <component name="PyNamespacePackagesService">
-    <option name="namespacePackageFolders">
-      <list>
-        <option value="$MODULE_DIR$/utils" />
-        <option value="$MODULE_DIR$/models" />
-      </list>
-    </option>
-  </component>
-</module>
\ No newline at end of file
diff --git a/.idea/deployment.xml b/.idea/deployment.xml
deleted file mode 100644
index cb75128..0000000
--- a/.idea/deployment.xml
+++ /dev/null
@@ -1,57 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="PublishConfigData" autoUpload="Always" serverName="houbo@exxact:22 DCSM" remoteFilesAllowedToDisappearOnAutoupload="false">
-    <serverData>
-      <paths name="BojianHou@157.139.115.48:22 password">
-        <serverdata>
-          <mappings>
-            <mapping local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-      <paths name="houbo@Titancomputers:22 password">
-        <serverdata>
-          <mappings>
-            <mapping local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-      <paths name="houbo@cubic-login.uphs.upenn.edu:22 password">
-        <serverdata>
-          <mappings>
-            <mapping local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-      <paths name="houbo@cubic-login.uphs.upenn.edu:22 password (1)">
-        <serverdata>
-          <mappings>
-            <mapping local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-      <paths name="houbo@exxact:22 DCSM">
-        <serverdata>
-          <mappings>
-            <mapping deploy="/Project/DCSM" local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-      <paths name="houbo@exxact:22 Vadesc">
-        <serverdata>
-          <mappings>
-            <mapping local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-      <paths name="houbo@exxact:22 password">
-        <serverdata>
-          <mappings>
-            <mapping local="$PROJECT_DIR$" web="/" />
-          </mappings>
-        </serverdata>
-      </paths>
-    </serverData>
-    <option name="myAutoUpload" value="ALWAYS" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
deleted file mode 100644
index 28a6be9..0000000
--- a/.idea/inspectionProfiles/Project_Default.xml
+++ /dev/null
@@ -1,89 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <profile version="1.0">
-    <option name="myName" value="Project Default" />
-    <inspection_tool class="PyCompatibilityInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <option name="ourVersions">
-        <value>
-          <list size="2">
-            <item index="0" class="java.lang.String" itemvalue="2.7" />
-            <item index="1" class="java.lang.String" itemvalue="3.10" />
-          </list>
-        </value>
-      </option>
-    </inspection_tool>
-    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <option name="ignoredPackages">
-        <value>
-          <list size="66">
-            <item index="0" class="java.lang.String" itemvalue="pandas" />
-            <item index="1" class="java.lang.String" itemvalue="scikit-learn" />
-            <item index="2" class="java.lang.String" itemvalue="numpy" />
-            <item index="3" class="java.lang.String" itemvalue="shap" />
-            <item index="4" class="java.lang.String" itemvalue="matplotlib" />
-            <item index="5" class="java.lang.String" itemvalue="tqdm" />
-            <item index="6" class="java.lang.String" itemvalue="transformers" />
-            <item index="7" class="java.lang.String" itemvalue="tensorflow" />
-            <item index="8" class="java.lang.String" itemvalue="seaborn" />
-            <item index="9" class="java.lang.String" itemvalue="scikit_learn" />
-            <item index="10" class="java.lang.String" itemvalue="python_Levenshtein" />
-            <item index="11" class="java.lang.String" itemvalue="torch" />
-            <item index="12" class="java.lang.String" itemvalue="Flask" />
-            <item index="13" class="java.lang.String" itemvalue="lifelines" />
-            <item index="14" class="java.lang.String" itemvalue="jupyter" />
-            <item index="15" class="java.lang.String" itemvalue="sklearn" />
-            <item index="16" class="java.lang.String" itemvalue="cvxpy" />
-            <item index="17" class="java.lang.String" itemvalue="googleapis-common-protos" />
-            <item index="18" class="java.lang.String" itemvalue="tabulate" />
-            <item index="19" class="java.lang.String" itemvalue="cvxopt" />
-            <item index="20" class="java.lang.String" itemvalue="promise" />
-            <item index="21" class="java.lang.String" itemvalue="theano" />
-            <item index="22" class="java.lang.String" itemvalue="source" />
-            <item index="23" class="java.lang.String" itemvalue="pastel" />
-            <item index="24" class="java.lang.String" itemvalue="docopt" />
-            <item index="25" class="java.lang.String" itemvalue="pydicom" />
-            <item index="26" class="java.lang.String" itemvalue="pylev" />
-            <item index="27" class="java.lang.String" itemvalue="multiprocess" />
-            <item index="28" class="java.lang.String" itemvalue="ruamel-yaml-clib" />
-            <item index="29" class="java.lang.String" itemvalue="crashtest" />
-            <item index="30" class="java.lang.String" itemvalue="pydicom-seg" />
-            <item index="31" class="java.lang.String" itemvalue="scs" />
-            <item index="32" class="java.lang.String" itemvalue="nibabel" />
-            <item index="33" class="java.lang.String" itemvalue="pyqt5-sip" />
-            <item index="34" class="java.lang.String" itemvalue="clikit" />
-            <item index="35" class="java.lang.String" itemvalue="h5py" />
-            <item index="36" class="java.lang.String" itemvalue="autograd-gamma" />
-            <item index="37" class="java.lang.String" itemvalue="pyqt5" />
-            <item index="38" class="java.lang.String" itemvalue="python-gdcm" />
-            <item index="39" class="java.lang.String" itemvalue="ecos" />
-            <item index="40" class="java.lang.String" itemvalue="attrs" />
-            <item index="41" class="java.lang.String" itemvalue="pyyaml" />
-            <item index="42" class="java.lang.String" itemvalue="autograd" />
-            <item index="43" class="java.lang.String" itemvalue="gdcm" />
-            <item index="44" class="java.lang.String" itemvalue="osqp" />
-            <item index="45" class="java.lang.String" itemvalue="progressbar" />
-            <item index="46" class="java.lang.String" itemvalue="opentsne" />
-            <item index="47" class="java.lang.String" itemvalue="numexpr" />
-            <item index="48" class="java.lang.String" itemvalue="simpleitk" />
-            <item index="49" class="java.lang.String" itemvalue="lasagne" />
-            <item index="50" class="java.lang.String" itemvalue="xgboost" />
-            <item index="51" class="java.lang.String" itemvalue="pyarrow" />
-            <item index="52" class="java.lang.String" itemvalue="opencv-python" />
-            <item index="53" class="java.lang.String" itemvalue="pyradiomics" />
-            <item index="54" class="java.lang.String" itemvalue="qdldl" />
-            <item index="55" class="java.lang.String" itemvalue="scikit-survival" />
-            <item index="56" class="java.lang.String" itemvalue="dill" />
-            <item index="57" class="java.lang.String" itemvalue="random-survival-forest" />
-            <item index="58" class="java.lang.String" itemvalue="dcmrtstruct2nii" />
-            <item index="59" class="java.lang.String" itemvalue="pykwalify" />
-            <item index="60" class="java.lang.String" itemvalue="importlib-resources" />
-            <item index="61" class="java.lang.String" itemvalue="future" />
-            <item index="62" class="java.lang.String" itemvalue="verstack" />
-            <item index="63" class="java.lang.String" itemvalue="ruamel-yaml" />
-            <item index="64" class="java.lang.String" itemvalue="cleo" />
-            <item index="65" class="java.lang.String" itemvalue="dm-tree" />
-          </list>
-        </value>
-      </option>
-    </inspection_tool>
-  </profile>
-</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 105ce2d..0000000
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 74cd65b..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Remote Python 3.8.12 (sftp://houbo@exxact:22/home/houbo/.conda/envs/hobo/bin/python)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 1db0bd5..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/Deep Clustering Survival Machines.iml" filepath="$PROJECT_DIR$/.idea/Deep Clustering Survival Machines.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/other.xml b/.idea/other.xml
deleted file mode 100644
index 640fd80..0000000
--- a/.idea/other.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="PySciProjectComponent">
-    <option name="PY_SCI_VIEW" value="true" />
-    <option name="PY_SCI_VIEW_SUGGESTED" value="true" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/remote-mappings.xml b/.idea/remote-mappings.xml
deleted file mode 100644
index 1487fac..0000000
--- a/.idea/remote-mappings.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="RemoteMappingsManager">
-    <list>
-      <list>
-        <remote-mappings server-id="python@sftp://houbo@exxact:22/home/houbo/.conda/envs/hobo/bin/python">
-          <settings>
-            <list>
-              <mapping local-root="$PROJECT_DIR$" remote-root="/home/houbo/Project/DCSM" />
-            </list>
-          </settings>
-        </remote-mappings>
-      </list>
-    </list>
-  </component>
-</project>
\ No newline at end of file