From 22f7cb34ee327a284d4ddb530f1d601670203aca Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Mon, 3 Oct 2022 13:07:44 -0700
Subject: [PATCH 01/12] test

---
 cmake/dependencies/ABLASTR.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cmake/dependencies/ABLASTR.cmake b/cmake/dependencies/ABLASTR.cmake
index aeb0abd44..2e1dbe0b2 100644
--- a/cmake/dependencies/ABLASTR.cmake
+++ b/cmake/dependencies/ABLASTR.cmake
@@ -29,6 +29,7 @@ macro(find_ablastr)
     # transitive control for openPMD/FFT/PICSAR superbuild
     # TODO (future)
 
+    # TODO: delete this
     # ABLASTR superbuild
     if(ImpactX_ablastr_internal OR ImpactX_ablastr_src)
         set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)

From d7e9ee76733b0df00e0a0c1846e73d437b1c614a Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 11:29:45 -0700
Subject: [PATCH 02/12] sync with mainline

---
 cmake/dependencies/ABLASTR.cmake | 1 -
 1 file changed, 1 deletion(-)

diff --git a/cmake/dependencies/ABLASTR.cmake b/cmake/dependencies/ABLASTR.cmake
index 2e1dbe0b2..aeb0abd44 100644
--- a/cmake/dependencies/ABLASTR.cmake
+++ b/cmake/dependencies/ABLASTR.cmake
@@ -29,7 +29,6 @@ macro(find_ablastr)
     # transitive control for openPMD/FFT/PICSAR superbuild
     # TODO (future)
 
-    # TODO: delete this
     # ABLASTR superbuild
     if(ImpactX_ablastr_internal OR ImpactX_ablastr_src)
         set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)

From 0ecbc309261a3509083d37efe626aaae56b2e4cc Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 13:46:57 -0700
Subject: [PATCH 03/12] Implement infrastructure for main files: - mad_var -
 mad_cmd - mad_elem - mad_macro

---
 src/madx/README.md    |  15 ++++++
 src/madx/mad_cmd.py   | 107 ++++++++++++++++++++++++++++++++++++++++++
 src/madx/mad_elem.py  |  90 +++++++++++++++++++++++++++++++++++
 src/madx/mad_macro.py |  45 ++++++++++++++++++
 src/madx/mad_var.py   |  83 ++++++++++++++++++++++++++++++++
 5 files changed, 340 insertions(+)
 create mode 100644 src/madx/README.md
 create mode 100644 src/madx/mad_cmd.py
 create mode 100644 src/madx/mad_elem.py
 create mode 100644 src/madx/mad_macro.py
 create mode 100644 src/madx/mad_var.py

diff --git a/src/madx/README.md b/src/madx/README.md
new file mode 100644
index 000000000..440425f36
--- /dev/null
+++ b/src/madx/README.md
@@ -0,0 +1,15 @@
+# MadX Python Interpreter (10/4/22)
+
+Author: Joey Zhu (https://github.com/np-eazy)
+
+This Python interpreter was written as a subset of MadX's C interpreter's full functionalities to suit the needs of ImpactX.
+Implementation contains a lot of boilerplate, but this is to maintain a reliable, verbatim approach for transcribing a large
+volume of code.
+
+### Supported objects
+- Variables
+- Elements
+- Macros (Lines)
+
+### Removed Functionalities
+- Fortran90 interface
\ No newline at end of file
diff --git a/src/madx/mad_cmd.py b/src/madx/mad_cmd.py
new file mode 100644
index 000000000..b4b70475d
--- /dev/null
+++ b/src/madx/mad_cmd.py
@@ -0,0 +1,107 @@
+class Command:
+    def __init__(self, name, module, group, stamp, link_type, mad8_type, beam_def, par_names, par):
+        self.name = name
+        self.module = module
+        self.group = group
+        self.stamp = stamp
+        self.link_type = link_type
+        self.mad8_type = mad8_type
+        self.beam_def = beam_def
+        self.par_names = par_names
+        self.par = par
+
+
+class CommandList:
+    def __init__(self, name, max_length):
+        self.name = name
+        self.lst = []
+        self.names = []
+        self.max_length = max_length
+
+    def add_var(self, var):
+        # TODO: add separately for names
+        self.lst += [var]
+
+
+class CommandListList:
+    def __init__(self, max_length):
+        self.lst = []
+        self.names = []
+        self.max_length = max_length
+
+    def add_var(self, var):
+        # TODO: add separately for names
+        self.lst += [var]
+
+
+# TODO: Implement functions as needed
+# Interface
+def new_command(name, nl_length, pl_length, module, group, link, mad_8):
+    return None
+
+def delete_command(command):
+    return None
+
+def clone_command(command):
+    return None
+
+def clone_command_flat(command):
+    return None
+
+def find_command(name, command_list):
+    return None
+
+
+# List Commands
+def new_command_list(name, max_length):
+    return CommandList(name, max_length)
+
+def delete_command_list(command_list):
+    return None
+
+def find_command_list(name, command_list_list):
+    return None
+
+def grow_command_list(command_list):
+    return None
+
+def add_to_command_list(label, command, command_list, flag):
+    return None
+
+def new_command_list_list(max_length):
+    return CommandListList(max_length)
+
+def add_to_command_list_list(label, command_list, command_list_list):
+    return None
+
+
+# Command Methods
+def exec_command():
+    return None
+
+def decode_command():
+    return None
+
+def dump_command(command): # For Debugging
+    return None
+
+def print_command(command):
+    return None
+
+def store_command_def(): # Processes command definition
+    return None
+
+def make_line(statement):
+    return None
+
+def get_stmt(file, supp_flag):
+    return None
+
+def get_defined_commands():
+    return None
+
+def remove_from_command_list(label, command_list):
+    return None
+
+def exec_add_expression(in_cmd):
+    return None
diff --git a/src/madx/mad_elem.py b/src/madx/mad_elem.py
new file mode 100644
index 000000000..08b3b1148
--- /dev/null
+++ b/src/madx/mad_elem.py
@@ -0,0 +1,90 @@
+class Element:
+    def __init__(self, name, def_type, bv, length, defi, parent, stamp, base_type, aperture, multipole):
+        self.name = name
+        self.def_type = def_type
+        self.bv = bv
+        self.length = length
+        self.defi = defi
+        self.parent = parent
+        self.stamp = stamp
+        self.base_type = base_type
+        self.aperture = aperture
+        self.multipole = multipole
+
+class ElementList:
+    def __init__(self, max_length):
+        self.lst = []
+        self.max_length = max_length
+
+    def add_var(self, var):
+        self.lst += [var]
+
+
+def make_element(name, parent, command, flag):
+    return None
+
+def clone_element(element):
+    return None
+
+def delete_element(element):
+    return None
+
+def update_element(element, update_command):
+    return None
+
+def update_element_children(element, update_command):
+    return None
+
+
+def dump_element(element):
+    return None
+
+def export_el_def(element, string, noexpr):
+    return None
+
+def export_el_def_8(element, string, noexpr):
+    return None
+
+
+def new_el_list(max_length):
+    return ElementList(max_length)
+
+def delete_el_list(el_list):
+    return None
+
+def find_element(name, el_list):
+    return None
+
+def write_elems(el_list, command_list, file, noexpr):
+    return None
+
+def write_elems_8(el_list, command_list, file):
+    return None
+
+
+def new_elem_node(element, occ_cnt):
+    return None
+
+def make_elem_node(element, occ_cnt):
+    return None
+
+def compound(e_name, occ_cnt):
+    return None
+
+
+def enter_element(in_cmd):
+    return None
+
+def element_name(name, l):
+    return None
+
+def element_value(node, params):
+    return None
+
+def element_vector(element, params, vector):
+    return None
+
+
+
+
+
diff --git a/src/madx/mad_macro.py b/src/madx/mad_macro.py
new file mode 100644
index 000000000..81b1961fb
--- /dev/null
+++ b/src/madx/mad_macro.py
@@ -0,0 +1,45 @@
+class Macro:
+    def __init__(self, name, n_formal, dead, formal, tokens, body, stamp, original):
+        self.name = name
+        self.n_formal = n_formal
+        self.dead = dead
+        self.formal = formal
+        self.tokens = tokens
+        self.body = body
+        self.stamp = stamp
+        self.original = original
+
+
+class MacroList:
+    def __init__(self, max_length):
+        self.lst = []
+        self.max_length = max_length
+
+    def add_var(self, var):
+        self.lst += [var]
+
+
+
+def make_macro(statemenet):
+    return None
+
+def new_macro(n_formal, length, p_length):
+    return None
+
+def new_macro_list(max_length):
+    return MacroList(max_length)
+
+def add_to_macro_list(macro, macro_list):
+    return None
+
+def disable_line(name, macro_list):
+    return None
+
+def replace_lines(macro, replace, reps):
+    return None
+
+def save_macros2file():
+    return None
+
+def exec_macro(in_cmd, pos):
+    return None
\ No newline at end of file
diff --git a/src/madx/mad_var.py b/src/madx/mad_var.py
new file mode 100644
index 000000000..46e9cdc02
--- /dev/null
+++ b/src/madx/mad_var.py
@@ -0,0 +1,83 @@
+class Constant:
+    def __init__(self, name, expr, value, stamp):
+        self.name = name
+        self.expr = expr
+        self.value = value
+        self.stamp = stamp
+
+
+class Variable:
+    def __init__(self, name, val, val_type, type, expression, string):
+        self.name = name
+        self.val = val
+        self.val_type = val_type
+        self.type = type
+        self.expression = expression
+        self.string = string
+
+
+class VariableList:
+    def __init__(self, max_length):
+        self.lst = []
+        self.max_length = max_length
+
+    def add_var(self, var):
+        self.lst += [var]
+
+
+# TODO: Implement as needed
+def enter_variable(in_cmd):
+    return None
+
+def new_variable(name, val, val_type, typ, expression, string):
+    return Variable(name, val, val_type, typ, expression, string)
+
+def variable_value(var):
+    return None
+
+
+def new_var_list(max_length):
+    return VariableList(max_length)
+
+def clone_var_list(var_list):
+    return None
+
+def delete_var_list(var_list):
+    return None
+
+def add_to_var_list(var, var_list, flag):
+    # TODO: Re-implement placeholder function var flag
+    var_list.add_var(var)
+
+def find_variable(name, var_list):
+    return None
+
+
+def make_string_variable(string):
+    return None
+
+def write_vars(var_list, command_list, file, noexpr):
+    return None
+
+def write_vars_8(var_list, command_list, file):
+    return None
+
+def set_variable(name, value):
+    return None
+
+def set_stringvar(name, string):
+    return None
+
+def get_variable(name):
+    return None
+
+def get_varstring(name):
+    return None
+
+def get_defined_constants():
+    return None
+
+
+
+
+

From caec449cf0a1c644a273ec0c8f386c99a628a108 Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 14:12:25 -0700
Subject: [PATCH 04/12] Implement core/global interpreter infrastructure: -
 mad_main - mad_gvar - mad_core: mad_init_c

---
 src/madx/mad_core.py | 208 +++++++++++++++++++++++++++++++++++++++++++
 src/madx/mad_gvar.py |  14 +++
 src/madx/mad_main.py |  19 ++++
 3 files changed, 241 insertions(+)
 create mode 100644 src/madx/mad_core.py
 create mode 100644 src/madx/mad_gvar.py
 create mode 100644 src/madx/mad_main.py

diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
new file mode 100644
index 000000000..54ad259d2
--- /dev/null
+++ b/src/madx/mad_core.py
@@ -0,0 +1,208 @@
+# include <signal.h>
+# include "madx.h"
+
+from mad_var import *
+from mad_elem import *
+from mad_macro import *
+from mad_cmd import *
+
+
+def mad_init_c(gvar):
+    # TODO: Implement subset of mad_init_c
+    # allocate variable ptr
+    ione = 1
+
+    # make stdout unbuffered for proper I/O synchronization with fortran
+    # setvbuf(stdout, 0, _IONBF, 0);
+    #
+    # init55(123456789);          /* random generator */
+    # if (watch_flag == 1)  debug_file = fopen("madx.debug", "w");
+    # else if (watch_flag == 2)  debug_file = stdout;
+    # if (stamp_flag == 1)  stamp_file = fopen("madx.stamp", "w");
+    # else if (stamp_flag == 2)  stamp_file = stdout;
+
+    # in = new_in_buff_list(100); /* list of input buffers, dynamic */
+
+    # // quick and dirty fix to accept jobs from filename
+    # in->input_files[0] = mad_argc > 1 ? fopen(mad_argv[1], "r") : stdin;
+    # if (!in->input_files[0]) {
+    # mad_error("invalid input filename ", " %s", mad_argv[1]);
+    # in->input_files[0] = stdin;
+    # }
+    # interactive = intrac();
+    # prt_file = stdout;
+    # pro = new_in_buff_list(100); /* list of process buffers, dynamic */
+    # pro->buffers[0] = new_in_buffer(IN_BUFF_SIZE);
+    # pro->curr = 1;
+    # c_dum = new_char_array(AUX_LG);
+    # c_join = new_char_array(AUX_LG);
+    # work = new_char_array(AUX_LG);
+    # l_wrk = new_char_array(AUX_LG);
+
+    # Physical Constants:
+    # deco_init();
+    # get_defined_constants();
+    # get_defined_commands(command_def);
+    # get_defined_commands(element_def);
+    # get_sxf_names();
+    #
+    # pi = get_variable("pi");
+    # twopi = two * pi;
+    # degrad = 180 / pi;
+    # raddeg = pi / 180;
+    # e = get_variable("e");
+    # clight = get_variable("clight");
+    # hbar = get_variable("hbar");
+
+    # Global Variable Initialization:
+    # aux_buff = new_char_array(AUX_LG);  /* dynamic temporary buffer */
+    gvar.variable_list = new_var_list(2000)  # dynamic list of variables
+    gvar.beam_list = new_command_list("beam_list", 10)  # dynamic beam list
+    gvar.table_deselect = new_command_list_list(10)  # dynamic
+    gvar.table_select = new_command_list_list(10)  # dynamic
+    gvar.defined_commands = new_command_list("defined_commands", 100)  # dynamic
+    gvar.stored_commands = new_command_list("stored_commands", 500)  # dynamic
+    gvar.line_list = new_macro_list(100)  # dynamic
+    gvar.macro_list = new_macro_list(100)  # dynamic
+    gvar.base_type_list = new_el_list(60)  # dynamic
+    gvar.element_list = new_el_list(20000)  # dynamic
+    # buffered_cmds = new_in_cmd_list(10000); /* dynamic */
+    # sequences = new_sequence_list(20); /* dynamic */
+    # match_sequs = new_sequence_list(2);
+    # selected_ranges = new_node_list(10000); /* dynamic */
+    gvar.selected_elements = new_el_list(10000)  # dynamic
+    # tmp_p_array = new_char_p_array(1000); /* dynamic */
+    # tmp_l_array = new_char_p_array(1000); /* dynamic */
+    # sxf_list = new_name_list("sxf_list", 50); /* dynamic */
+    # all_table_lists = new_table_list_list(10); /* dynamic */
+
+    # # Initialize needed work for commands
+    var = new_variable("twiss_tol", 1.e-6, 1, 1, None, None)
+    add_to_var_list(var, gvar.variable_list, 1)
+    # title = permbuff("no-title");
+    # set_defaults("option");
+    # if (interactive) { int false = 0; set_option("echo", &false); }
+    # set_defaults("beam");
+    # add_to_command_list("default_beam", current_beam, beam_list, 0);
+    # set_defaults("set");
+    # set_defaults("setplot");
+    # set_defaults("threader");
+    # table_register = new_table_list(10); /* dynamic */
+    # beta0_list = new_command_list("beta0_list", 10); /* dynamic */
+    # savebeta_list = new_command_list("savebeta_list", 10); /* dynamic */
+    # seqedit_select = /* dynamic - for "select seqedit" commands */
+    #     new_command_list("seqedit_select", 10);
+    # error_select = /* dynamic - for "select error" commands */
+    #     new_command_list("error-select", 10);
+    # save_select = /* dynamic - for "select save" commands */
+    #     new_command_list("save_select", 10);
+    # slice_select = /* dynamic - for "select makethin" commands */
+    #     new_command_list("slice_select", 10);
+    # sector_select = /* dynamic - for "select sectormap" commands */
+    #     new_command_list("sector_select", 10);
+    # interp_select = /* dynamic - for "select sectormap" commands */
+    #     new_command_list("interp_select", 10);
+    # s_range = new_int_array(10); /* dynamic */
+    # e_range = new_int_array(10); /* dynamic */
+    # sd_range = new_int_array(10); /* dynamic */
+    # ed_range = new_int_array(10); /* dynamic */
+    # zero_double(orbit0, 6);
+    # zero_double(disp0, 6);
+    # zero_double(guess_orbit,6);
+    # zero_double(oneturnmat, 36);
+    # set_option("twiss_print", &ione);
+    return None
+
+
+def madx_start(gvar):
+    # TODO: Implement normal madx_start
+
+    mad_init_c(gvar)
+
+    time = None
+    # /*  setbuf(stdout,(char *)0); */ /* no buffering - for debugging */
+    # time(&start_time); /* initialize timing */
+    # tm = localtime(&start_time); /* split system time */
+    # last_time = start_time;
+
+    # // compute padding of OSTYPE
+    # const char *pad[] = { "", " ", "  ", "    " };
+    # const int pad_sz = sizeof pad/sizeof *pad;
+    # int pad_idx = strlen("Windows")-strlen(version_ostype);
+    # if (pad_idx >= pad_sz) pad_idx = pad_sz-1;
+
+    #  printf("\n  ++++++++++++++++++++++++++++++++++++++++++++\n");
+    # printf("  +     MAD-X %s  (%s bit, %s) %s    +\n", version_name, version_arch, version_ostype, pad[pad_idx]);
+    # printf("  + Support: mad@cern.ch, http://cern.ch/mad +\n");
+    # printf("  + Release   date: %s               +\n", version_date);
+    # printf("  + Execution date: %04d.%02d.%02d %02d:%02d:%02d      +\n",
+    #        tm->tm_year+1900, tm->tm_mon+1, tm->tm_mday,
+    #                                            tm->tm_hour, tm->tm_min, tm->tm_sec);
+    # printf("  ++++++++++++++++++++++++++++++++++++++++++++\n");
+    # if (interactive) putchar('\n');
+    return None
+
+
+def madx_input(top):
+    # TODO: Implement normal madx_input
+    # TODO: Implement dynamic metadata lists
+    # {
+    #     fputs("This is where STDOUT is", stdout);
+    # if (interactive && in->curr == 0) fputs("X:> ", stdout);
+    # if (return_flag || get_stmt(in->input_files[in->curr], 0) == 0)
+    # {
+    # if (in->input_files[in->curr] != stdin) {
+    # fclose(in->input_files[in->curr]);
+    # in->input_files[in->curr] = 0;
+    # }
+    # if (in->curr == 0)
+    # return;
+    # else
+    #     in->curr -= 1;
+    # return_flag = 0;
+    # if (in->curr == top) return;
+    # }
+    # else
+    # {
+    # stolower_nq(in->buffers[in->curr]->c_a->c);
+    # pro_input(in->buffers[in->curr]->c_a->c);
+    # if (stop_flag)  return;
+    # }
+    # }
+    return None
+
+
+def madx_finish():
+    # TODO: Implement normal madx_finish
+    # TODO: Implement MadX-ImpactX Interface by dumping lists
+    # int warn_numb, warn_numbf, nwarnings;
+    #
+    # /* should work with Lahey on windows 24.03.2004 */
+    #
+    # match2_delete_expressions();
+    # match2_delete_arrays();
+    #
+    # if (final_message == 0)
+    #     {
+    #         final_message = 1;
+    # if (plots_made)
+    # {
+    #     gxterm_();
+    # }
+    # mad_err_getwarn(&warn_numb, &warn_numbf);
+    # nwarnings = warn_numb + warn_numbf;
+    # printf("\n  Number of warnings: %d\n",nwarnings);
+    # if (nwarnings > 0)
+    # {
+    #     printf("%d in C and %d in Fortran\n",warn_numb,warn_numbf);
+    # }
+    # if (get_option("trace")) time_stamp("end");
+    #
+    # // printf("poly-mul= %llu\n", poly_mul_count);
+    #
+    # printf("\n"
+    # "  ++++++++++++++++++++++++++++++++++++++++++++\n");
+    # printf("  +          MAD-X finished normally         +\n");
+    # printf("  ++++++++++++++++++++++++++++++++++++++++++++\n");
+    # }
+    return None
diff --git a/src/madx/mad_gvar.py b/src/madx/mad_gvar.py
new file mode 100644
index 000000000..39ba96a46
--- /dev/null
+++ b/src/madx/mad_gvar.py
@@ -0,0 +1,14 @@
+class GlobalVariable:
+    def __init__(self):
+        self.variable_list = None
+        self.beam_list = None
+        self.table_deselect = None
+        self.table_select = None
+        self.defined_commands = None
+        self.stored_commands = None
+        self.line_list = None
+        self.macro_list = None
+        self.base_type_list = None
+        self.element_list = None
+        self.selected_elements = None
+
diff --git a/src/madx/mad_main.py b/src/madx/mad_main.py
new file mode 100644
index 000000000..e8cc11d85
--- /dev/null
+++ b/src/madx/mad_main.py
@@ -0,0 +1,19 @@
+from mad_core import *
+import mad_gvar
+
+
+def mad_init():
+    madx_start(gvar)
+
+# TODO: Redefine function to take in gvar and filepath argument instead of int
+def mad_run(gvar, file=0):
+    madx_input(file)
+
+def mad_finish(gvar):
+    madx_finish()
+
+
+gvar = mad_gvar.GlobalVariable()
+mad_init()
+mad_run()
+mad_finish()
\ No newline at end of file

From 107a68a15fb549088f4671b73dd833ead849b63a Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 15:16:27 -0700
Subject: [PATCH 05/12] Reorganize files into directories, implement
 core/global interpreter infrastructure: - mad_core: madx_input

---
 src/madx/README.md                  |  5 +-
 src/madx/mad_core.py                | 59 +++++++++++----------
 src/madx/mad_main.py                | 18 ++++---
 src/madx/{ => objects}/mad_cmd.py   |  0
 src/madx/{ => objects}/mad_elem.py  |  0
 src/madx/{ => objects}/mad_gvar.py  |  3 ++
 src/madx/{ => objects}/mad_macro.py |  0
 src/madx/{ => objects}/mad_var.py   |  0
 src/madx/utils/mad_str.py           | 80 +++++++++++++++++++++++++++++
 9 files changed, 125 insertions(+), 40 deletions(-)
 rename src/madx/{ => objects}/mad_cmd.py (100%)
 rename src/madx/{ => objects}/mad_elem.py (100%)
 rename src/madx/{ => objects}/mad_gvar.py (86%)
 rename src/madx/{ => objects}/mad_macro.py (100%)
 rename src/madx/{ => objects}/mad_var.py (100%)
 create mode 100644 src/madx/utils/mad_str.py

diff --git a/src/madx/README.md b/src/madx/README.md
index 440425f36..37b6c3a81 100644
--- a/src/madx/README.md
+++ b/src/madx/README.md
@@ -11,5 +11,6 @@ volume of code.
 - Elements
 - Macros (Lines)
 
-### Removed Functionalities
-- Fortran90 interface
\ No newline at end of file
+### Removed/Changed Functionalities
+- stdin stdout char buffers are replaced with Python file read
+- Removed Fortran90 interface
\ No newline at end of file
diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 54ad259d2..3eb9b082d 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -1,10 +1,12 @@
 # include <signal.h>
 # include "madx.h"
 
-from mad_var import *
-from mad_elem import *
-from mad_macro import *
-from mad_cmd import *
+from src.madx.objects.mad_var import *
+from src.madx.objects.mad_elem import *
+from src.madx.objects.mad_macro import *
+from src.madx.objects.mad_cmd import *
+
+from src.madx.utils.mad_str import *
 
 
 def mad_init_c(gvar):
@@ -143,36 +145,33 @@ def madx_start(gvar):
     return None
 
 
-def madx_input(top):
-    # TODO: Implement normal madx_input
+def madx_input(filename, gvar):
     # TODO: Implement dynamic metadata lists
-    # {
-    #     fputs("This is where STDOUT is", stdout);
-    # if (interactive && in->curr == 0) fputs("X:> ", stdout);
-    # if (return_flag || get_stmt(in->input_files[in->curr], 0) == 0)
-    # {
-    # if (in->input_files[in->curr] != stdin) {
-    # fclose(in->input_files[in->curr]);
-    # in->input_files[in->curr] = 0;
-    # }
-    # if (in->curr == 0)
-    # return;
-    # else
-    #     in->curr -= 1;
-    # return_flag = 0;
-    # if (in->curr == top) return;
-    # }
-    # else
-    # {
-    # stolower_nq(in->buffers[in->curr]->c_a->c);
-    # pro_input(in->buffers[in->curr]->c_a->c);
-    # if (stop_flag)  return;
-    # }
-    # }
+
+    # The original MadX file uses charbuffers, but in the Python version we want to keep
+    # implementation simple with filenames and char lists, and whatever equivalent looping
+    # logic. We assume that given ImpactX's use case, there is only one case for the input:
+    # That is, anything and everything is in file_content, so we don't have to do any buffer logic.
+    file_content = []
+    with open(filename, 'r') as f:
+        file_content += [f.read()]
+    i = 0
+    in_stop = False
+    while not in_stop:
+        stolower_nq(file_content, i)
+
+        # TODO: Figure out exactly where pro_input is defined. This is the entry point into the interpreter logic
+        # pro_input(file_content, i)
+        if gvar.stop_flag:
+            return
+
+        in_stop = i < len(file_content)
+        i += 1  # whenever a buffer char is popped for interpreter
+
     return None
 
 
-def madx_finish():
+def madx_finish(gvar):
     # TODO: Implement normal madx_finish
     # TODO: Implement MadX-ImpactX Interface by dumping lists
     # int warn_numb, warn_numbf, nwarnings;
diff --git a/src/madx/mad_main.py b/src/madx/mad_main.py
index e8cc11d85..7a15e9d21 100644
--- a/src/madx/mad_main.py
+++ b/src/madx/mad_main.py
@@ -1,19 +1,21 @@
 from mad_core import *
-import mad_gvar
+from src.madx.objects import mad_gvar
 
 
-def mad_init():
+def mad_init(gvar):
     madx_start(gvar)
 
+
 # TODO: Redefine function to take in gvar and filepath argument instead of int
 def mad_run(gvar, file=0):
-    madx_input(file)
+    madx_input(file, gvar)
+
 
 def mad_finish(gvar):
-    madx_finish()
+    madx_finish(gvar)
 
 
-gvar = mad_gvar.GlobalVariable()
-mad_init()
-mad_run()
-mad_finish()
\ No newline at end of file
+global_variable = mad_gvar.GlobalVariable()
+mad_init(global_variable)
+mad_run(global_variable)
+mad_finish(global_variable)
diff --git a/src/madx/mad_cmd.py b/src/madx/objects/mad_cmd.py
similarity index 100%
rename from src/madx/mad_cmd.py
rename to src/madx/objects/mad_cmd.py
diff --git a/src/madx/mad_elem.py b/src/madx/objects/mad_elem.py
similarity index 100%
rename from src/madx/mad_elem.py
rename to src/madx/objects/mad_elem.py
diff --git a/src/madx/mad_gvar.py b/src/madx/objects/mad_gvar.py
similarity index 86%
rename from src/madx/mad_gvar.py
rename to src/madx/objects/mad_gvar.py
index 39ba96a46..b15c9e9e4 100644
--- a/src/madx/mad_gvar.py
+++ b/src/madx/objects/mad_gvar.py
@@ -12,3 +12,6 @@ def __init__(self):
         self.element_list = None
         self.selected_elements = None
 
+        self.return_flag = False
+        self.stop_flag = False
+
diff --git a/src/madx/mad_macro.py b/src/madx/objects/mad_macro.py
similarity index 100%
rename from src/madx/mad_macro.py
rename to src/madx/objects/mad_macro.py
diff --git a/src/madx/mad_var.py b/src/madx/objects/mad_var.py
similarity index 100%
rename from src/madx/mad_var.py
rename to src/madx/objects/mad_var.py
diff --git a/src/madx/utils/mad_str.py b/src/madx/utils/mad_str.py
new file mode 100644
index 000000000..a2ef05206
--- /dev/null
+++ b/src/madx/utils/mad_str.py
@@ -0,0 +1,80 @@
+def myatof(input):
+    return None
+
+def mycpy(sout, sin):
+    return None
+
+def mystrchr(input, c):
+    return None
+
+def mystrcpy(target, source):
+    return None
+
+def mystrstr(string, s):
+    return None
+
+def myrepl(char_in, char_out, string_in, string_out):
+    return None
+
+def mysplit(buf, list):
+    return None
+
+
+
+def conv_char(string, tint):
+    return None
+
+def stolower_nq(string, i):
+    return string
+
+def strip(name):
+    return None
+
+def supp_lt(inbuf, flag):
+    return 0
+
+def supp_mul_char(c, string):
+    return None
+
+# Suppress trailing blanks in string
+def supp_tb(string):
+    return None
+
+# Return whether String defaults to 0
+def zero_string(string):
+    return False
+
+# Copy string to allocated buffer, strdump
+def tmpbuff(string):
+    return string
+
+def buffer(string):
+    return tmpbuff(string)
+
+def permbuff(string):
+    return buffer(string)
+
+def join(it_list, n):
+    return ""
+
+def join_b(it_list, n):
+    return ""
+
+def next_non_blank(string):
+    return ''
+
+def next_non_blank_pos(string):
+    return 0
+
+def noquote(string):
+    return string
+
+def quote_level(string, send):
+    return 0
+
+def square_to_colon(string):
+    return 0
+
+def slash_to_bkslash(string):
+    return string
+

From 582258d408bd0528470a20137c794183c16de701 Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 15:23:25 -0700
Subject: [PATCH 06/12] Finish organizing mad_core infrastructure

---
 src/madx/mad_core.py | 71 ++++++++++----------------------------------
 1 file changed, 15 insertions(+), 56 deletions(-)

diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 3eb9b082d..2360b3f32 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -117,36 +117,13 @@ def mad_init_c(gvar):
 
 
 def madx_start(gvar):
-    # TODO: Implement normal madx_start
 
     mad_init_c(gvar)
 
-    time = None
-    # /*  setbuf(stdout,(char *)0); */ /* no buffering - for debugging */
-    # time(&start_time); /* initialize timing */
-    # tm = localtime(&start_time); /* split system time */
-    # last_time = start_time;
-
-    # // compute padding of OSTYPE
-    # const char *pad[] = { "", " ", "  ", "    " };
-    # const int pad_sz = sizeof pad/sizeof *pad;
-    # int pad_idx = strlen("Windows")-strlen(version_ostype);
-    # if (pad_idx >= pad_sz) pad_idx = pad_sz-1;
-
-    #  printf("\n  ++++++++++++++++++++++++++++++++++++++++++++\n");
-    # printf("  +     MAD-X %s  (%s bit, %s) %s    +\n", version_name, version_arch, version_ostype, pad[pad_idx]);
-    # printf("  + Support: mad@cern.ch, http://cern.ch/mad +\n");
-    # printf("  + Release   date: %s               +\n", version_date);
-    # printf("  + Execution date: %04d.%02d.%02d %02d:%02d:%02d      +\n",
-    #        tm->tm_year+1900, tm->tm_mon+1, tm->tm_mday,
-    #                                            tm->tm_hour, tm->tm_min, tm->tm_sec);
-    # printf("  ++++++++++++++++++++++++++++++++++++++++++++\n");
-    # if (interactive) putchar('\n');
     return None
 
 
 def madx_input(filename, gvar):
-    # TODO: Implement dynamic metadata lists
 
     # The original MadX file uses charbuffers, but in the Python version we want to keep
     # implementation simple with filenames and char lists, and whatever equivalent looping
@@ -158,9 +135,11 @@ def madx_input(filename, gvar):
     i = 0
     in_stop = False
     while not in_stop:
+        # TODO: Implement dynamic metadata lists
+        # We don't need line numbers per se, just the order of buffer consumption is enough for metadata.
         stolower_nq(file_content, i)
 
-        # TODO: Figure out exactly where pro_input is defined. This is the entry point into the interpreter logic
+        # TODO: Figure out exactly where pro_input is defined. This is the entry point into the interpreter logic but isn't clearly defined in the source code.
         # pro_input(file_content, i)
         if gvar.stop_flag:
             return
@@ -172,36 +151,16 @@ def madx_input(filename, gvar):
 
 
 def madx_finish(gvar):
-    # TODO: Implement normal madx_finish
-    # TODO: Implement MadX-ImpactX Interface by dumping lists
-    # int warn_numb, warn_numbf, nwarnings;
-    #
-    # /* should work with Lahey on windows 24.03.2004 */
-    #
-    # match2_delete_expressions();
-    # match2_delete_arrays();
-    #
-    # if (final_message == 0)
-    #     {
-    #         final_message = 1;
-    # if (plots_made)
-    # {
-    #     gxterm_();
-    # }
-    # mad_err_getwarn(&warn_numb, &warn_numbf);
-    # nwarnings = warn_numb + warn_numbf;
-    # printf("\n  Number of warnings: %d\n",nwarnings);
-    # if (nwarnings > 0)
-    # {
-    #     printf("%d in C and %d in Fortran\n",warn_numb,warn_numbf);
-    # }
-    # if (get_option("trace")) time_stamp("end");
-    #
-    # // printf("poly-mul= %llu\n", poly_mul_count);
-    #
-    # printf("\n"
-    # "  ++++++++++++++++++++++++++++++++++++++++++++\n");
-    # printf("  +          MAD-X finished normally         +\n");
-    # printf("  ++++++++++++++++++++++++++++++++++++++++++++\n");
-    # }
+    for variable in gvar.variable_list:
+        # TODO: Convert variable into ImpactX known type and add to other lists
+        variable = variable
+
+    for element in gvar.el_list:
+        # TODO: Convert element into ImpactX known type and add to other lists
+        element = element
+
+    for line in gvar.line_list:
+        # TODO: Convert line into ImpactX known type and add to other lists
+        line = line
+
     return None

From ecc22c7cc51f4a82561aed1ce612d1e6d67497fd Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 15:28:05 -0700
Subject: [PATCH 07/12] Finish organizing mad_core infrastructure, re-organized
 TODOs

---
 src/madx/README.md            | 5 ++++-
 src/madx/mad_core.py          | 1 -
 src/madx/mad_main.py          | 1 -
 src/madx/objects/mad_cmd.py   | 4 +---
 src/madx/objects/mad_elem.py  | 1 +
 src/madx/objects/mad_gvar.py  | 1 +
 src/madx/objects/mad_macro.py | 1 +
 src/madx/objects/mad_var.py   | 3 +--
 src/madx/utils/mad_str.py     | 1 +
 9 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/madx/README.md b/src/madx/README.md
index 37b6c3a81..4d3e5ef12 100644
--- a/src/madx/README.md
+++ b/src/madx/README.md
@@ -13,4 +13,7 @@ volume of code.
 
 ### Removed/Changed Functionalities
 - stdin stdout char buffers are replaced with Python file read
-- Removed Fortran90 interface
\ No newline at end of file
+- Removed Fortran90 interface
+
+### Other dev notes
+- Execution begins at mad_main.py
\ No newline at end of file
diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 2360b3f32..8c534bdd9 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -10,7 +10,6 @@
 
 
 def mad_init_c(gvar):
-    # TODO: Implement subset of mad_init_c
     # allocate variable ptr
     ione = 1
 
diff --git a/src/madx/mad_main.py b/src/madx/mad_main.py
index 7a15e9d21..5dfc50bc3 100644
--- a/src/madx/mad_main.py
+++ b/src/madx/mad_main.py
@@ -6,7 +6,6 @@ def mad_init(gvar):
     madx_start(gvar)
 
 
-# TODO: Redefine function to take in gvar and filepath argument instead of int
 def mad_run(gvar, file=0):
     madx_input(file, gvar)
 
diff --git a/src/madx/objects/mad_cmd.py b/src/madx/objects/mad_cmd.py
index b4b70475d..7824c1e97 100644
--- a/src/madx/objects/mad_cmd.py
+++ b/src/madx/objects/mad_cmd.py
@@ -1,3 +1,4 @@
+# TODO: Implement on-demand
 class Command:
     def __init__(self, name, module, group, stamp, link_type, mad8_type, beam_def, par_names, par):
         self.name = name
@@ -19,7 +20,6 @@ def __init__(self, name, max_length):
         self.max_length = max_length
 
     def add_var(self, var):
-        # TODO: add separately for names
         self.lst += [var]
 
 
@@ -30,11 +30,9 @@ def __init__(self, max_length):
         self.max_length = max_length
 
     def add_var(self, var):
-        # TODO: add separately for names
         self.lst += [var]
 
 
-# TODO: Implement functions as needed
 # Interface
 def new_command(name, nl_length, pl_length, module, group, link, mad_8):
     return None
diff --git a/src/madx/objects/mad_elem.py b/src/madx/objects/mad_elem.py
index 08b3b1148..c38c73bbb 100644
--- a/src/madx/objects/mad_elem.py
+++ b/src/madx/objects/mad_elem.py
@@ -1,3 +1,4 @@
+# TODO: Implement on-demand
 class Element:
     def __init__(self, name, def_type, bv, length, defi, parent, stamp, base_type, aperture, multipole):
         self.name = name
diff --git a/src/madx/objects/mad_gvar.py b/src/madx/objects/mad_gvar.py
index b15c9e9e4..99abd5e25 100644
--- a/src/madx/objects/mad_gvar.py
+++ b/src/madx/objects/mad_gvar.py
@@ -1,3 +1,4 @@
+# TODO: Implement on-demand
 class GlobalVariable:
     def __init__(self):
         self.variable_list = None
diff --git a/src/madx/objects/mad_macro.py b/src/madx/objects/mad_macro.py
index 81b1961fb..bfc1206a4 100644
--- a/src/madx/objects/mad_macro.py
+++ b/src/madx/objects/mad_macro.py
@@ -1,3 +1,4 @@
+# TODO: Implement on-demand
 class Macro:
     def __init__(self, name, n_formal, dead, formal, tokens, body, stamp, original):
         self.name = name
diff --git a/src/madx/objects/mad_var.py b/src/madx/objects/mad_var.py
index 46e9cdc02..ec35af110 100644
--- a/src/madx/objects/mad_var.py
+++ b/src/madx/objects/mad_var.py
@@ -1,3 +1,4 @@
+# TODO: Implement on-demand
 class Constant:
     def __init__(self, name, expr, value, stamp):
         self.name = name
@@ -25,7 +26,6 @@ def add_var(self, var):
         self.lst += [var]
 
 
-# TODO: Implement as needed
 def enter_variable(in_cmd):
     return None
 
@@ -46,7 +46,6 @@ def delete_var_list(var_list):
     return None
 
 def add_to_var_list(var, var_list, flag):
-    # TODO: Re-implement placeholder function var flag
     var_list.add_var(var)
 
 def find_variable(name, var_list):
diff --git a/src/madx/utils/mad_str.py b/src/madx/utils/mad_str.py
index a2ef05206..89aae979e 100644
--- a/src/madx/utils/mad_str.py
+++ b/src/madx/utils/mad_str.py
@@ -25,6 +25,7 @@ def conv_char(string, tint):
     return None
 
 def stolower_nq(string, i):
+    # TODO: Implement this and other string processing algorithms as needed
     return string
 
 def strip(name):

From db52b8ea2abd3672849215cc56bb71cdb7d11231 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Oct 2022 22:28:21 +0000
Subject: [PATCH 08/12] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/madx/README.md            |  2 +-
 src/madx/mad_core.py          |  9 ++++-----
 src/madx/mad_main.py          |  1 +
 src/madx/objects/mad_cmd.py   | 27 ++++++++++++++++++++++++---
 src/madx/objects/mad_elem.py  | 35 +++++++++++++++++++++++++++++------
 src/madx/objects/mad_gvar.py  |  1 -
 src/madx/objects/mad_macro.py | 10 ++++++++--
 src/madx/objects/mad_var.py   | 18 +++++++++++++-----
 src/madx/utils/mad_str.py     | 27 ++++++++++++++++++++++++---
 9 files changed, 104 insertions(+), 26 deletions(-)

diff --git a/src/madx/README.md b/src/madx/README.md
index 4d3e5ef12..f2d3716e3 100644
--- a/src/madx/README.md
+++ b/src/madx/README.md
@@ -16,4 +16,4 @@ volume of code.
 - Removed Fortran90 interface
 
 ### Other dev notes
-- Execution begins at mad_main.py
\ No newline at end of file
+- Execution begins at mad_main.py
diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 8c534bdd9..22cdd1b3a 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -1,11 +1,10 @@
 # include <signal.h>
 # include "madx.h"
 
-from src.madx.objects.mad_var import *
+from src.madx.objects.mad_cmd import *
 from src.madx.objects.mad_elem import *
 from src.madx.objects.mad_macro import *
-from src.madx.objects.mad_cmd import *
-
+from src.madx.objects.mad_var import *
 from src.madx.utils.mad_str import *
 
 
@@ -78,7 +77,7 @@ def mad_init_c(gvar):
     # all_table_lists = new_table_list_list(10); /* dynamic */
 
     # # Initialize needed work for commands
-    var = new_variable("twiss_tol", 1.e-6, 1, 1, None, None)
+    var = new_variable("twiss_tol", 1.0e-6, 1, 1, None, None)
     add_to_var_list(var, gvar.variable_list, 1)
     # title = permbuff("no-title");
     # set_defaults("option");
@@ -129,7 +128,7 @@ def madx_input(filename, gvar):
     # logic. We assume that given ImpactX's use case, there is only one case for the input:
     # That is, anything and everything is in file_content, so we don't have to do any buffer logic.
     file_content = []
-    with open(filename, 'r') as f:
+    with open(filename, "r") as f:
         file_content += [f.read()]
     i = 0
     in_stop = False
diff --git a/src/madx/mad_main.py b/src/madx/mad_main.py
index 5dfc50bc3..a8450c46b 100644
--- a/src/madx/mad_main.py
+++ b/src/madx/mad_main.py
@@ -1,4 +1,5 @@
 from mad_core import *
+
 from src.madx.objects import mad_gvar
 
 
diff --git a/src/madx/objects/mad_cmd.py b/src/madx/objects/mad_cmd.py
index 7824c1e97..98ef9a3df 100644
--- a/src/madx/objects/mad_cmd.py
+++ b/src/madx/objects/mad_cmd.py
@@ -1,6 +1,8 @@
 # TODO: Implement on-demand
 class Command:
-    def __init__(self, name, module, group, stamp, link_type, mad8_type, beam_def, par_names, par):
+    def __init__(
+        self, name, module, group, stamp, link_type, mad8_type, beam_def, par_names, par
+    ):
         self.name = name
         self.module = module
         self.group = group
@@ -37,15 +39,19 @@ def add_var(self, var):
 def new_command(name, nl_length, pl_length, module, group, link, mad_8):
     return None
 
+
 def delete_command(command):
     return None
 
+
 def clone_command(command):
     return None
 
+
 def clone_command_flat(command):
     return None
 
+
 def find_command(name, command_list):
     return None
 
@@ -54,21 +60,27 @@ def find_command(name, command_list):
 def new_command_list(name, max_length):
     return CommandList(name, max_length)
 
+
 def delete_command_list(command_list):
     return None
 
+
 def find_command_list(name, command_list_list):
     return None
 
+
 def grow_command_list(command_list):
     return None
 
+
 def add_to_command_list(label, command, command_list, flag):
     return None
 
+
 def new_command_list_list(max_length):
     return CommandListList(max_length)
 
+
 def add_to_command_list_list(label, command_list, command_list_list):
     return None
 
@@ -77,29 +89,38 @@ def add_to_command_list_list(label, command_list, command_list_list):
 def exec_command():
     return None
 
+
 def decode_command():
     return None
 
-def dump_command(command): # For Debugging
+
+def dump_command(command):  # For Debugging
     return None
 
+
 def print_command(command):
     return None
 
-def store_command_def(): # Processes command definition
+
+def store_command_def():  # Processes command definition
     return None
 
+
 def make_line(statement):
     return None
 
+
 def get_stmt(file, supp_flag):
     return None
 
+
 def get_defined_commands():
     return None
 
+
 def remove_from_command_list(label, command_list):
     return None
 
+
 def exec_add_expression(in_cmd):
     return None
diff --git a/src/madx/objects/mad_elem.py b/src/madx/objects/mad_elem.py
index c38c73bbb..178158621 100644
--- a/src/madx/objects/mad_elem.py
+++ b/src/madx/objects/mad_elem.py
@@ -1,6 +1,18 @@
 # TODO: Implement on-demand
 class Element:
-    def __init__(self, name, def_type, bv, length, defi, parent, stamp, base_type, aperture, multipole):
+    def __init__(
+        self,
+        name,
+        def_type,
+        bv,
+        length,
+        defi,
+        parent,
+        stamp,
+        base_type,
+        aperture,
+        multipole,
+    ):
         self.name = name
         self.def_type = def_type
         self.bv = bv
@@ -12,6 +24,7 @@ def __init__(self, name, def_type, bv, length, defi, parent, stamp, base_type, a
         self.aperture = aperture
         self.multipole = multipole
 
+
 class ElementList:
     def __init__(self, max_length):
         self.lst = []
@@ -24,15 +37,19 @@ def add_var(self, var):
 def make_element(name, parent, command, flag):
     return None
 
+
 def clone_element(element):
     return None
 
+
 def delete_element(element):
     return None
 
+
 def update_element(element, update_command):
     return None
 
+
 def update_element_children(element, update_command):
     return None
 
@@ -40,9 +57,11 @@ def update_element_children(element, update_command):
 def dump_element(element):
     return None
 
+
 def export_el_def(element, string, noexpr):
     return None
 
+
 def export_el_def_8(element, string, noexpr):
     return None
 
@@ -50,15 +69,19 @@ def export_el_def_8(element, string, noexpr):
 def new_el_list(max_length):
     return ElementList(max_length)
 
+
 def delete_el_list(el_list):
     return None
 
+
 def find_element(name, el_list):
     return None
 
+
 def write_elems(el_list, command_list, file, noexpr):
     return None
 
+
 def write_elems_8(el_list, command_list, file):
     return None
 
@@ -66,9 +89,11 @@ def write_elems_8(el_list, command_list, file):
 def new_elem_node(element, occ_cnt):
     return None
 
+
 def make_elem_node(element, occ_cnt):
     return None
 
+
 def compound(e_name, occ_cnt):
     return None
 
@@ -76,16 +101,14 @@ def compound(e_name, occ_cnt):
 def enter_element(in_cmd):
     return None
 
+
 def element_name(name, l):
     return None
 
+
 def element_value(node, params):
     return None
 
+
 def element_vector(element, params, vector):
     return None
-
-
-
-
-
diff --git a/src/madx/objects/mad_gvar.py b/src/madx/objects/mad_gvar.py
index 99abd5e25..2c59fc473 100644
--- a/src/madx/objects/mad_gvar.py
+++ b/src/madx/objects/mad_gvar.py
@@ -15,4 +15,3 @@ def __init__(self):
 
         self.return_flag = False
         self.stop_flag = False
-
diff --git a/src/madx/objects/mad_macro.py b/src/madx/objects/mad_macro.py
index bfc1206a4..3e317cb6d 100644
--- a/src/madx/objects/mad_macro.py
+++ b/src/madx/objects/mad_macro.py
@@ -20,27 +20,33 @@ def add_var(self, var):
         self.lst += [var]
 
 
-
 def make_macro(statemenet):
     return None
 
+
 def new_macro(n_formal, length, p_length):
     return None
 
+
 def new_macro_list(max_length):
     return MacroList(max_length)
 
+
 def add_to_macro_list(macro, macro_list):
     return None
 
+
 def disable_line(name, macro_list):
     return None
 
+
 def replace_lines(macro, replace, reps):
     return None
 
+
 def save_macros2file():
     return None
 
+
 def exec_macro(in_cmd, pos):
-    return None
\ No newline at end of file
+    return None
diff --git a/src/madx/objects/mad_var.py b/src/madx/objects/mad_var.py
index ec35af110..17cedc518 100644
--- a/src/madx/objects/mad_var.py
+++ b/src/madx/objects/mad_var.py
@@ -29,9 +29,11 @@ def add_var(self, var):
 def enter_variable(in_cmd):
     return None
 
+
 def new_variable(name, val, val_type, typ, expression, string):
     return Variable(name, val, val_type, typ, expression, string)
 
+
 def variable_value(var):
     return None
 
@@ -39,15 +41,19 @@ def variable_value(var):
 def new_var_list(max_length):
     return VariableList(max_length)
 
+
 def clone_var_list(var_list):
     return None
 
+
 def delete_var_list(var_list):
     return None
 
+
 def add_to_var_list(var, var_list, flag):
     var_list.add_var(var)
 
+
 def find_variable(name, var_list):
     return None
 
@@ -55,28 +61,30 @@ def find_variable(name, var_list):
 def make_string_variable(string):
     return None
 
+
 def write_vars(var_list, command_list, file, noexpr):
     return None
 
+
 def write_vars_8(var_list, command_list, file):
     return None
 
+
 def set_variable(name, value):
     return None
 
+
 def set_stringvar(name, string):
     return None
 
+
 def get_variable(name):
     return None
 
+
 def get_varstring(name):
     return None
 
+
 def get_defined_constants():
     return None
-
-
-
-
-
diff --git a/src/madx/utils/mad_str.py b/src/madx/utils/mad_str.py
index 89aae979e..d46caedfa 100644
--- a/src/madx/utils/mad_str.py
+++ b/src/madx/utils/mad_str.py
@@ -1,81 +1,102 @@
 def myatof(input):
     return None
 
+
 def mycpy(sout, sin):
     return None
 
+
 def mystrchr(input, c):
     return None
 
+
 def mystrcpy(target, source):
     return None
 
+
 def mystrstr(string, s):
     return None
 
+
 def myrepl(char_in, char_out, string_in, string_out):
     return None
 
+
 def mysplit(buf, list):
     return None
 
 
-
 def conv_char(string, tint):
     return None
 
+
 def stolower_nq(string, i):
     # TODO: Implement this and other string processing algorithms as needed
     return string
 
+
 def strip(name):
     return None
 
+
 def supp_lt(inbuf, flag):
     return 0
 
+
 def supp_mul_char(c, string):
     return None
 
+
 # Suppress trailing blanks in string
 def supp_tb(string):
     return None
 
+
 # Return whether String defaults to 0
 def zero_string(string):
     return False
 
+
 # Copy string to allocated buffer, strdump
 def tmpbuff(string):
     return string
 
+
 def buffer(string):
     return tmpbuff(string)
 
+
 def permbuff(string):
     return buffer(string)
 
+
 def join(it_list, n):
     return ""
 
+
 def join_b(it_list, n):
     return ""
 
+
 def next_non_blank(string):
-    return ''
+    return ""
+
 
 def next_non_blank_pos(string):
     return 0
 
+
 def noquote(string):
     return string
 
+
 def quote_level(string, send):
     return 0
 
+
 def square_to_colon(string):
     return 0
 
+
 def slash_to_bkslash(string):
     return string
-

From e199d3bc938697e6ab06763f217278d442f005f4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Oct 2022 22:28:21 +0000
Subject: [PATCH 09/12] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/madx/README.md            |  2 +-
 src/madx/mad_core.py          |  9 ++++-----
 src/madx/mad_main.py          |  1 +
 src/madx/objects/mad_cmd.py   | 27 ++++++++++++++++++++++++---
 src/madx/objects/mad_elem.py  | 35 +++++++++++++++++++++++++++++------
 src/madx/objects/mad_gvar.py  |  1 -
 src/madx/objects/mad_macro.py | 10 ++++++++--
 src/madx/objects/mad_var.py   | 18 +++++++++++++-----
 src/madx/utils/mad_str.py     | 29 ++++++++++++++++++++++++++---
 9 files changed, 106 insertions(+), 26 deletions(-)

diff --git a/src/madx/README.md b/src/madx/README.md
index 4d3e5ef12..f2d3716e3 100644
--- a/src/madx/README.md
+++ b/src/madx/README.md
@@ -16,4 +16,4 @@ volume of code.
 - Removed Fortran90 interface
 
 ### Other dev notes
-- Execution begins at mad_main.py
\ No newline at end of file
+- Execution begins at mad_main.py
diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 8c534bdd9..22cdd1b3a 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -1,11 +1,10 @@
 # include <signal.h>
 # include "madx.h"
 
-from src.madx.objects.mad_var import *
+from src.madx.objects.mad_cmd import *
 from src.madx.objects.mad_elem import *
 from src.madx.objects.mad_macro import *
-from src.madx.objects.mad_cmd import *
-
+from src.madx.objects.mad_var import *
 from src.madx.utils.mad_str import *
 
 
@@ -78,7 +77,7 @@ def mad_init_c(gvar):
     # all_table_lists = new_table_list_list(10); /* dynamic */
 
     # # Initialize needed work for commands
-    var = new_variable("twiss_tol", 1.e-6, 1, 1, None, None)
+    var = new_variable("twiss_tol", 1.0e-6, 1, 1, None, None)
     add_to_var_list(var, gvar.variable_list, 1)
     # title = permbuff("no-title");
     # set_defaults("option");
@@ -129,7 +128,7 @@ def madx_input(filename, gvar):
     # logic. We assume that given ImpactX's use case, there is only one case for the input:
     # That is, anything and everything is in file_content, so we don't have to do any buffer logic.
     file_content = []
-    with open(filename, 'r') as f:
+    with open(filename, "r") as f:
         file_content += [f.read()]
     i = 0
     in_stop = False
diff --git a/src/madx/mad_main.py b/src/madx/mad_main.py
index 5dfc50bc3..a8450c46b 100644
--- a/src/madx/mad_main.py
+++ b/src/madx/mad_main.py
@@ -1,4 +1,5 @@
 from mad_core import *
+
 from src.madx.objects import mad_gvar
 
 
diff --git a/src/madx/objects/mad_cmd.py b/src/madx/objects/mad_cmd.py
index 7824c1e97..98ef9a3df 100644
--- a/src/madx/objects/mad_cmd.py
+++ b/src/madx/objects/mad_cmd.py
@@ -1,6 +1,8 @@
 # TODO: Implement on-demand
 class Command:
-    def __init__(self, name, module, group, stamp, link_type, mad8_type, beam_def, par_names, par):
+    def __init__(
+        self, name, module, group, stamp, link_type, mad8_type, beam_def, par_names, par
+    ):
         self.name = name
         self.module = module
         self.group = group
@@ -37,15 +39,19 @@ def add_var(self, var):
 def new_command(name, nl_length, pl_length, module, group, link, mad_8):
     return None
 
+
 def delete_command(command):
     return None
 
+
 def clone_command(command):
     return None
 
+
 def clone_command_flat(command):
     return None
 
+
 def find_command(name, command_list):
     return None
 
@@ -54,21 +60,27 @@ def find_command(name, command_list):
 def new_command_list(name, max_length):
     return CommandList(name, max_length)
 
+
 def delete_command_list(command_list):
     return None
 
+
 def find_command_list(name, command_list_list):
     return None
 
+
 def grow_command_list(command_list):
     return None
 
+
 def add_to_command_list(label, command, command_list, flag):
     return None
 
+
 def new_command_list_list(max_length):
     return CommandListList(max_length)
 
+
 def add_to_command_list_list(label, command_list, command_list_list):
     return None
 
@@ -77,29 +89,38 @@ def add_to_command_list_list(label, command_list, command_list_list):
 def exec_command():
     return None
 
+
 def decode_command():
     return None
 
-def dump_command(command): # For Debugging
+
+def dump_command(command):  # For Debugging
     return None
 
+
 def print_command(command):
     return None
 
-def store_command_def(): # Processes command definition
+
+def store_command_def():  # Processes command definition
     return None
 
+
 def make_line(statement):
     return None
 
+
 def get_stmt(file, supp_flag):
     return None
 
+
 def get_defined_commands():
     return None
 
+
 def remove_from_command_list(label, command_list):
     return None
 
+
 def exec_add_expression(in_cmd):
     return None
diff --git a/src/madx/objects/mad_elem.py b/src/madx/objects/mad_elem.py
index c38c73bbb..178158621 100644
--- a/src/madx/objects/mad_elem.py
+++ b/src/madx/objects/mad_elem.py
@@ -1,6 +1,18 @@
 # TODO: Implement on-demand
 class Element:
-    def __init__(self, name, def_type, bv, length, defi, parent, stamp, base_type, aperture, multipole):
+    def __init__(
+        self,
+        name,
+        def_type,
+        bv,
+        length,
+        defi,
+        parent,
+        stamp,
+        base_type,
+        aperture,
+        multipole,
+    ):
         self.name = name
         self.def_type = def_type
         self.bv = bv
@@ -12,6 +24,7 @@ def __init__(self, name, def_type, bv, length, defi, parent, stamp, base_type, a
         self.aperture = aperture
         self.multipole = multipole
 
+
 class ElementList:
     def __init__(self, max_length):
         self.lst = []
@@ -24,15 +37,19 @@ def add_var(self, var):
 def make_element(name, parent, command, flag):
     return None
 
+
 def clone_element(element):
     return None
 
+
 def delete_element(element):
     return None
 
+
 def update_element(element, update_command):
     return None
 
+
 def update_element_children(element, update_command):
     return None
 
@@ -40,9 +57,11 @@ def update_element_children(element, update_command):
 def dump_element(element):
     return None
 
+
 def export_el_def(element, string, noexpr):
     return None
 
+
 def export_el_def_8(element, string, noexpr):
     return None
 
@@ -50,15 +69,19 @@ def export_el_def_8(element, string, noexpr):
 def new_el_list(max_length):
     return ElementList(max_length)
 
+
 def delete_el_list(el_list):
     return None
 
+
 def find_element(name, el_list):
     return None
 
+
 def write_elems(el_list, command_list, file, noexpr):
     return None
 
+
 def write_elems_8(el_list, command_list, file):
     return None
 
@@ -66,9 +89,11 @@ def write_elems_8(el_list, command_list, file):
 def new_elem_node(element, occ_cnt):
     return None
 
+
 def make_elem_node(element, occ_cnt):
     return None
 
+
 def compound(e_name, occ_cnt):
     return None
 
@@ -76,16 +101,14 @@ def compound(e_name, occ_cnt):
 def enter_element(in_cmd):
     return None
 
+
 def element_name(name, l):
     return None
 
+
 def element_value(node, params):
     return None
 
+
 def element_vector(element, params, vector):
     return None
-
-
-
-
-
diff --git a/src/madx/objects/mad_gvar.py b/src/madx/objects/mad_gvar.py
index 99abd5e25..2c59fc473 100644
--- a/src/madx/objects/mad_gvar.py
+++ b/src/madx/objects/mad_gvar.py
@@ -15,4 +15,3 @@ def __init__(self):
 
         self.return_flag = False
         self.stop_flag = False
-
diff --git a/src/madx/objects/mad_macro.py b/src/madx/objects/mad_macro.py
index bfc1206a4..3e317cb6d 100644
--- a/src/madx/objects/mad_macro.py
+++ b/src/madx/objects/mad_macro.py
@@ -20,27 +20,33 @@ def add_var(self, var):
         self.lst += [var]
 
 
-
 def make_macro(statemenet):
     return None
 
+
 def new_macro(n_formal, length, p_length):
     return None
 
+
 def new_macro_list(max_length):
     return MacroList(max_length)
 
+
 def add_to_macro_list(macro, macro_list):
     return None
 
+
 def disable_line(name, macro_list):
     return None
 
+
 def replace_lines(macro, replace, reps):
     return None
 
+
 def save_macros2file():
     return None
 
+
 def exec_macro(in_cmd, pos):
-    return None
\ No newline at end of file
+    return None
diff --git a/src/madx/objects/mad_var.py b/src/madx/objects/mad_var.py
index ec35af110..17cedc518 100644
--- a/src/madx/objects/mad_var.py
+++ b/src/madx/objects/mad_var.py
@@ -29,9 +29,11 @@ def add_var(self, var):
 def enter_variable(in_cmd):
     return None
 
+
 def new_variable(name, val, val_type, typ, expression, string):
     return Variable(name, val, val_type, typ, expression, string)
 
+
 def variable_value(var):
     return None
 
@@ -39,15 +41,19 @@ def variable_value(var):
 def new_var_list(max_length):
     return VariableList(max_length)
 
+
 def clone_var_list(var_list):
     return None
 
+
 def delete_var_list(var_list):
     return None
 
+
 def add_to_var_list(var, var_list, flag):
     var_list.add_var(var)
 
+
 def find_variable(name, var_list):
     return None
 
@@ -55,28 +61,30 @@ def find_variable(name, var_list):
 def make_string_variable(string):
     return None
 
+
 def write_vars(var_list, command_list, file, noexpr):
     return None
 
+
 def write_vars_8(var_list, command_list, file):
     return None
 
+
 def set_variable(name, value):
     return None
 
+
 def set_stringvar(name, string):
     return None
 
+
 def get_variable(name):
     return None
 
+
 def get_varstring(name):
     return None
 
+
 def get_defined_constants():
     return None
-
-
-
-
-
diff --git a/src/madx/utils/mad_str.py b/src/madx/utils/mad_str.py
index 89aae979e..aaab68ec3 100644
--- a/src/madx/utils/mad_str.py
+++ b/src/madx/utils/mad_str.py
@@ -1,81 +1,104 @@
 def myatof(input):
     return None
 
+
 def mycpy(sout, sin):
     return None
 
+
 def mystrchr(input, c):
     return None
 
+
 def mystrcpy(target, source):
     return None
 
+
 def mystrstr(string, s):
     return None
 
+
 def myrepl(char_in, char_out, string_in, string_out):
     return None
 
+
 def mysplit(buf, list):
     return None
 
 
-
 def conv_char(string, tint):
     return None
 
+
 def stolower_nq(string, i):
     # TODO: Implement this and other string processing algorithms as needed
     return string
 
+
 def strip(name):
     return None
 
+
 def supp_lt(inbuf, flag):
     return 0
 
+
 def supp_mul_char(c, string):
     return None
 
+
 # Suppress trailing blanks in string
 def supp_tb(string):
     return None
 
+
 # Return whether String defaults to 0
 def zero_string(string):
     return False
 
+
 # Copy string to allocated buffer, strdump
 def tmpbuff(string):
     return string
 
+
 def buffer(string):
     return tmpbuff(string)
 
+
 def permbuff(string):
     return buffer(string)
 
+def is_token(pb, string, string_length):
+    return False
+
 def join(it_list, n):
     return ""
 
+
 def join_b(it_list, n):
     return ""
 
+
 def next_non_blank(string):
-    return ''
+    return ""
+
 
 def next_non_blank_pos(string):
     return 0
 
+
 def noquote(string):
     return string
 
+
 def quote_level(string, send):
     return 0
 
+
 def square_to_colon(string):
     return 0
 
+
 def slash_to_bkslash(string):
     return string
-

From bcf62f46f1b30f56fea165831a0cf8ca73ed394a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Oct 2022 22:35:00 +0000
Subject: [PATCH 10/12] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/madx/utils/mad_str.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/madx/utils/mad_str.py b/src/madx/utils/mad_str.py
index 38ea804da..0770cc605 100644
--- a/src/madx/utils/mad_str.py
+++ b/src/madx/utils/mad_str.py
@@ -69,6 +69,7 @@ def buffer(string):
 def permbuff(string):
     return buffer(string)
 
+
 def is_token(pb, string, string_length):
     return False
 

From 80fdde0745cfb7fc751abea37fdaa139672b423b Mon Sep 17 00:00:00 2001
From: Joey Zhu <joey.j.zhu@gmail.com>
Date: Tue, 4 Oct 2022 15:43:27 -0700
Subject: [PATCH 11/12] add mad_eval file

---
 src/madx/interpreter/mad_eval.py | 4 ++++
 src/madx/mad_core.py             | 6 ++++--
 2 files changed, 8 insertions(+), 2 deletions(-)
 create mode 100644 src/madx/interpreter/mad_eval.py

diff --git a/src/madx/interpreter/mad_eval.py b/src/madx/interpreter/mad_eval.py
new file mode 100644
index 000000000..6acbaac05
--- /dev/null
+++ b/src/madx/interpreter/mad_eval.py
@@ -0,0 +1,4 @@
+def pro_input(file_content, i):
+    # TODO: This is where the parsing logic starts!!!
+    return None
+
diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 22cdd1b3a..0cf0f8943 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -6,6 +6,7 @@
 from src.madx.objects.mad_macro import *
 from src.madx.objects.mad_var import *
 from src.madx.utils.mad_str import *
+from src.madx.interpreter.mad_eval import *
 
 
 def mad_init_c(gvar):
@@ -137,8 +138,9 @@ def madx_input(filename, gvar):
         # We don't need line numbers per se, just the order of buffer consumption is enough for metadata.
         stolower_nq(file_content, i)
 
-        # TODO: Figure out exactly where pro_input is defined. This is the entry point into the interpreter logic but isn't clearly defined in the source code.
-        # pro_input(file_content, i)
+        # TODO: Figure out exactly where pro_input is defined. This is the entry point into the interpreter logic but
+        #  isn't clearly defined in the source code.
+        pro_input(file_content, i)
         if gvar.stop_flag:
             return
 

From 6671ac6db7aa78ff1f50df85c13f7e09c79dc5da Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Oct 2022 22:43:56 +0000
Subject: [PATCH 12/12] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/madx/interpreter/mad_eval.py | 1 -
 src/madx/mad_core.py             | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/madx/interpreter/mad_eval.py b/src/madx/interpreter/mad_eval.py
index 6acbaac05..ffaa0e290 100644
--- a/src/madx/interpreter/mad_eval.py
+++ b/src/madx/interpreter/mad_eval.py
@@ -1,4 +1,3 @@
 def pro_input(file_content, i):
     # TODO: This is where the parsing logic starts!!!
     return None
-
diff --git a/src/madx/mad_core.py b/src/madx/mad_core.py
index 0cf0f8943..fc4bd8156 100644
--- a/src/madx/mad_core.py
+++ b/src/madx/mad_core.py
@@ -1,12 +1,12 @@
 # include <signal.h>
 # include "madx.h"
 
+from src.madx.interpreter.mad_eval import *
 from src.madx.objects.mad_cmd import *
 from src.madx.objects.mad_elem import *
 from src.madx.objects.mad_macro import *
 from src.madx.objects.mad_var import *
 from src.madx.utils.mad_str import *
-from src.madx.interpreter.mad_eval import *
 
 
 def mad_init_c(gvar):