Merge remote-tracking branch 'origin/main' into romanov_new_alchemy

.github/workflows/python-tests.yml

@@ -5,15 +5,15 @@ on: [push]
 jobs:
   build:
 
-    runs-on: ubuntu:20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -26,4 +26,11 @@ jobs:
         run: |
           cd $GITHUB_WORKSPACE/python
           python -m unittest discover -s $GITHUB_WORKSPACE/python/tests -t $GITHUB_WORKSPACE/python/tests
-          
+
+      - name: Test CLI commands
+        run: |          
+          source environment.bash
+          echo "rcnd command is running"
+          rcnd --help
+          echo "rcdb command is running"
+          rcdb --help

bin/rcdb

@@ -1,3 +1,15 @@
-#!/bin/sh
+#!/usr/bin/env python3
 
-/usr/bin/env python3 $RCDB_HOME/python/rcdb/rcdb_cli "$@"
+import os
+import sys
+
+# Figure out where is python directory
+this_file_dir = os.path.dirname(os.path.abspath(__file__))
+python_dir = os.path.join(this_file_dir, '..', 'python')
+
+# Add the directory to the Python modules search path
+sys.path.insert(0, python_dir)
+
+# Import and run rcdb
+from rcdb.rcdb_cli.app import rcdb_cli
+rcdb_cli(prog_name="rcdb")

bin/rcnd

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import importlib.util
+
+# Figure out where is rcnd.py located
+this_file_dir = os.path.dirname(os.path.abspath(__file__))
+
+this_file_dir = os.path.dirname(os.path.abspath(__file__))
+python_dir = os.path.join(this_file_dir, '..', 'python')
+
+# Add the directory to the Python modules search path
+sys.path.insert(0, python_dir)
+
+module_path = os.path.join(this_file_dir, '..', 'python', 'utilites', 'rcnd.py')
+module_path = os.path.abspath(module_path)
+
+# Load the module from the specified file
+spec = importlib.util.spec_from_file_location('rcnd', module_path)
+rcnd = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(rcnd)
+
+# Now you can use functions from the module
+rcnd.main()

cpp/include/RCDB/SQLiteCpp.h

@@ -159,78 +159,6 @@ namespace SQLite
 
 
 }  // namespace SQLite
-/**
- * @file    VariadicBind.h
- * @ingroup SQLiteCpp
- * @brief   Convenience function for Statement::bind(...)
- *
- * Copyright (c) 2016 Paul Dreik ([email protected])
- * Copyright (c) 2016 Sebastien Rombauts ([email protected])
- *
- * Distributed under the MIT License (MIT) (See accompanying file LICENSE.txt
- * or copy at http://opensource.org/licenses/MIT)
- */
-
-#if (__cplusplus >= 201402L) || ( defined(_MSC_VER) && (_MSC_VER >= 1900) ) // c++14: Visual Studio 2015
-
-
-/// @cond
-#include <initializer_list>
-
-namespace SQLite
-{
-
-/// implementation detail for variadic bind.
-namespace detail {
-template<class F, class ...Args, std::size_t ... I>
-inline void invoke_with_index(F&& f, std::integer_sequence<std::size_t, I...>, const Args& ...args)
-{
-    std::initializer_list<int> { (f(I+1, args), 0)... };
-}
-
-/// implementation detail for variadic bind.
-template<class F, class ...Args>
-inline void invoke_with_index(F&& f, const Args& ... args)
-{
-    invoke_with_index(std::forward<F>(f), std::index_sequence_for<Args...>(), args...);
-}
-
-} // namespace detail
-/// @endcond
-
-/**
- * \brief Convenience function for calling Statement::bind(...) once for each argument given.
- *
- * This takes care of incrementing the index between each calls to bind.
- *
- * This feature requires a c++14 capable compiler.
- *
- * \code{.cpp}
- * SQLite::Statement stm("SELECT * FROM MyTable WHERE colA>? && colB=? && colC<?");
- * bind(stm,a,b,c);
- * //...is equivalent to
- * stm.bind(1,a);
- * stm.bind(2,b);
- * stm.bind(3,c);
- * \endcode
- * @param s statement
- * @param args one or more args to bind.
- */
-template<class ...Args>
-void bind(SQLite::Statement& s, const Args& ... args)
-{
-    static_assert(sizeof...(args) > 0, "please invoke bind with one or more args");
-
-    auto f=[&s](std::size_t index, const auto& value)
-    {
-        s.bind(index, value);
-    };
-    detail::invoke_with_index(f, args...);
-}
-
-}  // namespace SQLite
-
-#endif // c++14
 
 /**
  * @file    Statement.h
@@ -876,6 +804,81 @@ namespace SQLite
 
 
 }  // namespace SQLite
+
+/**
+ * @file    VariadicBind.h
+ * @ingroup SQLiteCpp
+ * @brief   Convenience function for Statement::bind(...)
+ *
+ * Copyright (c) 2016 Paul Dreik ([email protected])
+ * Copyright (c) 2016 Sebastien Rombauts ([email protected])
+ *
+ * Distributed under the MIT License (MIT) (See accompanying file LICENSE.txt
+ * or copy at http://opensource.org/licenses/MIT)
+ */
+
+#if (__cplusplus >= 201402L) || ( defined(_MSC_VER) && (_MSC_VER >= 1900) ) // c++14: Visual Studio 2015
+
+
+/// @cond
+#include <initializer_list>
+
+namespace SQLite
+{
+
+/// implementation detail for variadic bind.
+namespace detail {
+template<class F, class ...Args, std::size_t ... I>
+inline void invoke_with_index(F&& f, std::integer_sequence<std::size_t, I...>, const Args& ...args)
+{
+    std::initializer_list<int> { (f(I+1, args), 0)... };
+}
+
+/// implementation detail for variadic bind.
+template<class F, class ...Args>
+inline void invoke_with_index(F&& f, const Args& ... args)
+{
+    invoke_with_index(std::forward<F>(f), std::index_sequence_for<Args...>(), args...);
+}
+
+} // namespace detail
+/// @endcond
+
+/**
+ * \brief Convenience function for calling Statement::bind(...) once for each argument given.
+ *
+ * This takes care of incrementing the index between each calls to bind.
+ *
+ * This feature requires a c++14 capable compiler.
+ *
+ * \code{.cpp}
+ * SQLite::Statement stm("SELECT * FROM MyTable WHERE colA>? && colB=? && colC<?");
+ * bind(stm,a,b,c);
+ * //...is equivalent to
+ * stm.bind(1,a);
+ * stm.bind(2,b);
+ * stm.bind(3,c);
+ * \endcode
+ * @param s statement
+ * @param args one or more args to bind.
+ */
+template<class ...Args>
+void bind(SQLite::Statement& s, const Args& ... args)
+{
+    static_assert(sizeof...(args) > 0, "please invoke bind with one or more args");
+
+    auto f=[&s](std::size_t index, const auto& value)
+    {
+        s.bind(index, value);
+    };
+    detail::invoke_with_index(f, args...);
+}
+
+}  // namespace SQLite
+
+#endif // c++14
+
+
 /**
  * @file    Column.h
  * @ingroup SQLiteCpp
@@ -2908,4 +2911,4 @@ namespace SQLite
 
 }  // namespace SQLite
 
-#endif // SQLITE_CPP_HEADER_
+#endif // SQLITE_CPP_HEADER_

cpp/include/RCDB/SqLiteProvider.h

@@ -6,7 +6,7 @@
 #define RCDB_CPP_SQLITEPROVIDER_H
 
 #include <sqlite3.h>
-#include <SQLiteCpp/SQLiteCpp.h>
+#include "SQLiteCpp.h"
 #include <iostream>
 #include <memory>
 #include "DataProvider.h"

cpp/include/RCDB/StringUtils.h

@@ -38,12 +38,12 @@ class StringUtils {
 
     // trim from start (in place)
     static inline void ltrim(std::string &s) {
-        s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
+        s.erase(s.begin(), std::find_if(s.begin(), s.end(), [](char c) { return !isspace(c); }));
     }
 
     // trim from end (in place)
     static inline void rtrim(std::string &s) {
-        s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
+        s.erase(std::find_if(s.rbegin(), s.rend(), [](char c) { return !isspace(c); }).base(), s.end());
     }
 
     // trim from both ends (in place)

python/rcdb/__init__.py

@@ -2,7 +2,7 @@
 from .provider import RCDBProvider
 from .provider import ConfigurationProvider
 from .rcdb_cli.app import rcdb_cli as run_rcdb_cli
-
+from .errors import *
 
 # This thing separates cells in data blob
 blob_delimiter = "|"

python/rcdb/rcdb_cli/ls.py

@@ -11,9 +11,7 @@
 def ls(context, search, is_long):
     """Lists conditions"""
 
-    print(context)
-    exit(0)
-
+
     db = context.db
     assert isinstance(db, RCDBProvider)
     cnd_types = db.get_condition_types_by_name()

python/tests/test_coda_parser.py

@@ -12,7 +12,7 @@ class TestCodaParser(unittest.TestCase):
     """ Tests ConditionType, ConditionValue classes and their operations in provider"""
 
     def setUp(self):
-        self.this_dir = os.path.dirname(inspect.getfile(test_get_runs))
+        self.this_dir = os.path.dirname(__file__)
         self.this_dir = os.path.normpath(self.this_dir)
 
     def test_parse_intermediate_file(self):

python/utilites/rcnd.py

@@ -217,7 +217,7 @@ def new_run(db, run_number):
     print("Created run number {}".format(run_number))
 
 
-if __name__ == "__main__":
+def main():
     parser = argparse.ArgumentParser(description=help_text, epilog=examples,
                                      formatter_class=RawDescriptionHelpFormatter)
     parser.add_argument("-c", "--connection", help="Connection string to database", metavar='<string>', default="")
@@ -320,3 +320,6 @@ def new_run(db, run_number):
         log.debug("No run_number, no condition_name. Show stats")
         print_stats(rcdb_db)
         exit(0)
+
+if __name__ == "__main__":
+    main()