Add void to empty parameter list (#9)

* Finished C89/C90/C95/C99 support. Version can only be switched in kernel or with magics. Might be worth having separate kernels for each standard.

* Added option to link maths library. On by default.

* Fixed empty input error. Now input loops until there is input with length > 0.

.dockerignore

@@ -0,0 +1,10 @@
+__pycache__
+*.pyc
+build/
+dist/
+MANIFEST
+.idea/
+.ipynb_checkpoints/
+*.egg-info/
+.git
+.gitignore

.gitignore

@@ -3,4 +3,7 @@ __pycache__
 build/
 dist/
 MANIFEST
-.idea/
+.idea/
+.ipynb_checkpoints/
+*.egg-info/
+venv/

Dockerfile

@@ -1,8 +1,19 @@
 FROM jupyter/minimal-notebook
-MAINTAINER Brendan Rius <ping@brendan-rius.com>
+MAINTAINER Xaver Klemenschits <klemenschits@iue.tuwien.ac.at>
 
 USER root
 
-COPY ./ /home/$NB_USER/.jupyter/jupyter_c_kernel/
-RUN pip install /home/$NB_USER/.jupyter/jupyter_c_kernel/
-RUN jupyter-kernelspec install /home/$NB_USER/.jupyter/jupyter_c_kernel/c_spec/
+# Install vim and ssh
+RUN apt-get update
+RUN apt-get install -y vim openssh-client
+
+WORKDIR /tmp
+
+COPY ./ jupyter_c_kernel/
+
+RUN pip install --no-cache-dir -e jupyter_c_kernel/ > piplog.txt
+RUN cd jupyter_c_kernel && install_c_kernel --user > installlog.txt
+
+WORKDIR /home/$NB_USER/
+
+USER $NB_USER

MANIFEST.in

@@ -0,0 +1,3 @@
+include jupyter_c_kernel/resources/master.c
+include jupyter_c_kernel/resources/stdio_wrap.h
+include README.md LICENSE.txt

README.md

@@ -1,28 +1,82 @@
-# Minimal C kernel for Jupyter
+# C kernel for Jupyter
+
+This project was forked from [https://github.com/brendan-rius/jupyter-c-kernel](brendan-rius/jupyter-c-kernel) as that project seems to have been abandoned. (PR is pending)
+
+This project includes fixes to many issues reported in [https://github.com/brendan-rius/jupyter-c-kernel](brendan-rius/jupyter-c-kernel), as well as the following additional features:
+
+* Option for buffered output to mimic command line behaviour (useful for teaching, default is on)
+* Command line input via `scanf` and `getchar`
+* Support for `C89`/`ANSI C` (all newer versions were already supported and still are)
+
+Following limitations compared to command line execution exist:
+
+* Input is always buffered due to limitations of the jupyter interface
+* When using `-ansi` or `-std=C89`, glibc still has to support at least `C99` for the interfacing with jupyter (this should not be an issue on an OS made after 2000)
 
 ## Use with Docker (recommended)
 
- * `docker pull brendanrius/jupyter-c-kernel`
- * `docker run -d -p 8888:8888 brendanrius/jupyter-c-kernel`
- * Go to [http://localhost:8888](http://localhost:8888) (or your VM address if you are using Docker Machine)
+* `docker pull xaverklemenschits/jupyter-c-kernel`
+* `docker run -p 8888:8888 xaverklemenschits/jupyter-c-kernel`
+* Copy the given URL containing the token, and browse to it. For instance:
+
+ ```bash
+ Copy/paste this URL into your browser when you connect for the first time,
+ to login with a token:
+    http://localhost:8888/?token=66750c80bd0788f6ba15760aadz53beb9a9fb4cf8ac15ce8
+ ```
 
 ## Manual installation
 
- * Make sure you have the following requirements installed:
+Works only on Linux and OS X. Windows is not supported yet. If you want to use this project on Windows, please use Docker.
+
+* Make sure you have the following requirements installed:
   * gcc
   * jupyter
-  * python
+  * python 3
   * pip
- * `git clone git@github.com:brendan-rius/jupyter-c-kernel.git`
- * `pip install jupyter-c-kernel`
- * `cd jupyter-c-kernel`
- * `jupyter-kernelspec install c_spec/`
- * `jupyter-notebook`. Enjoy!
+
+### Step-by-step
+
+```bash
+git clone https://github.com/XaverKlemenschits/jupyter-c-kernel.git
+cd jupyter-c-kernel
+pip install -e .  # for system install: sudo install .
+cd jupyter_c_kernel && install_c_kernel --user # for sys install: sudo install_c_kernel
+# now you can start the notebook
+jupyter notebook
+```
 
 ## Example of notebook
 
 ![Example of notebook](example-notebook.png?raw=true "Example of notebook")
 
+## Custom compilation flags
+
+You can use custom compilation flags like so:
+
+![Custom compulation flag](custom_flags.png?raw=true "Example of notebook using custom compilation flags")
+
+Here, the `-lm` flag is passed so you can use the math library.
+
+## Contributing
+
+The docker image installs the kernel in editable mode, meaning that you can
+change the code in real-time in Docker. For that, just run the docker box like
+that:
+
+```bash
+git clone https://github.com/XaverKlemenschits/jupyter-c-kernel.git
+cd jupyter-c-kernel
+docker build -t myName/jupyter .
+docker run -v $(pwd):/tmp/jupyter_c_kernel/ -p 8888:8888 myName/jupyter
+```
+
+This clones the source, run the kernel, and binds the current folder (the one
+you just cloned) to the corresponding folder in Docker.
+Now, if you change the source, it will be reflected in [http://localhost:8888](http://localhost:8888)
+instantly. Do not forget to click "restart" the kernel on the page as it does
+not auto-restart.
+
 ## License
 
-[MIT](LICENSE.txt)
+[MIT](LICENSE.txt)

c_spec/kernel.json

@@ -1,11 +0,0 @@
-{
-  "argv": [
-    "python",
-    "-m",
-    "c_kernel",
-    "-f",
-    "{connection_file}"
-  ],
-  "display_name": "C",
-  "language": "c"
-}

example-notebook.ipynb

@@ -10,9 +10,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -32,6 +30,7 @@
     "\n",
     "int main() {\n",
     "    printf(\"Hello world\\n\");\n",
+    "    return 0;\n",
     "}"
    ]
   },
@@ -52,9 +51,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -98,9 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -142,14 +137,14 @@
   "kernelspec": {
    "display_name": "C",
    "language": "c",
-   "name": "c_kernel"
+   "name": "c"
   },
   "language_info": {
-   "file_extension": "c",
+   "file_extension": ".c",
    "mimetype": "text/plain",
-   "name": "c"
+   "name": "text/x-c++src"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }

jupyter_c_kernel/install_c_kernel

@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+import json
+import os
+import sys
+import argparse
+
+from jupyter_client.kernelspec import KernelSpecManager
+from IPython.utils.tempdir import TemporaryDirectory
+
+kernel_json = {
+    "argv": [
+        "python3",
+        "-m",
+        "jupyter_c_kernel",
+        "-f",
+        "{connection_file}"
+    ],
+    "display_name": "C",
+    "language": "c"
+}
+
+
+def install_my_kernel_spec(user=True, prefix=None):
+    with TemporaryDirectory() as td:
+        os.chmod(td, 0o755)  # Starts off as 700, not user readable
+        with open(os.path.join(td, 'kernel.json'), 'w') as f:
+            json.dump(kernel_json, f, sort_keys=True)
+        # TODO: Copy resources once they're specified
+
+        print('Installing IPython kernel spec')
+        KernelSpecManager().install_kernel_spec(td, 'c', user=user, prefix=prefix)
+
+
+def _is_root():
+    try:
+        return os.geteuid() == 0
+    except AttributeError:
+        return False  # assume not an admin on non-Unix platforms
+
+
+def main(argv=[]):
+    parser = argparse.ArgumentParser(
+        description='Install KernelSpec for C Kernel'
+    )
+    prefix_locations = parser.add_mutually_exclusive_group()
+
+    prefix_locations.add_argument(
+        '--user',
+        help='Install KernelSpec in user homedirectory',
+        action='store_false' if _is_root() else 'store_true'
+    )
+    prefix_locations.add_argument(
+        '--sys-prefix',
+        help='Install KernelSpec in sys.prefix. Useful in conda / virtualenv',
+        action='store_true',
+        dest='sys_prefix'
+    )
+    prefix_locations.add_argument(
+        '--prefix',
+        help='Install KernelSpec in this prefix',
+        default=None
+    )
+
+    args = parser.parse_args()
+
+    if args.sys_prefix:
+        prefix = sys.prefix
+        user = None
+    elif args.user:
+        prefix = None
+        user = True
+    else:
+        prefix = args.prefix
+        user = None
+
+    install_my_kernel_spec(user=user, prefix=prefix)
+
+
+if __name__ == '__main__':
+    main(argv=sys.argv)

jupyter_c_kernel/kernel.py

@@ -1,7 +1,88 @@
+from queue import Queue
+from threading import Thread
+
 from ipykernel.kernelbase import Kernel
+import re
 import subprocess
 import tempfile
 import os
+import os.path as path
+
+
+class RealTimeSubprocess(subprocess.Popen):
+    """
+    A subprocess that allows to read its stdout and stderr in real time
+    """
+
+    inputRequest = "<inputRequest>"
+
+    def __init__(self, cmd, write_to_stdout, write_to_stderr, read_from_stdin):
+        """
+        :param cmd: the command to execute
+        :param write_to_stdout: a callable that will be called with chunks of data from stdout
+        :param write_to_stderr: a callable that will be called with chunks of data from stderr
+        """
+        self._write_to_stdout = write_to_stdout
+        self._write_to_stderr = write_to_stderr
+        self._read_from_stdin = read_from_stdin
+
+        super().__init__(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE, bufsize=0)
+
+        self._stdout_queue = Queue()
+        self._stdout_thread = Thread(target=RealTimeSubprocess._enqueue_output, args=(self.stdout, self._stdout_queue))
+        self._stdout_thread.daemon = True
+        self._stdout_thread.start()
+
+        self._stderr_queue = Queue()
+        self._stderr_thread = Thread(target=RealTimeSubprocess._enqueue_output, args=(self.stderr, self._stderr_queue))
+        self._stderr_thread.daemon = True
+        self._stderr_thread.start()
+
+    @staticmethod
+    def _enqueue_output(stream, queue):
+        """
+        Add chunks of data from a stream to a queue until the stream is empty.
+        """
+        for line in iter(lambda: stream.read(4096), b''):
+            queue.put(line)
+        stream.close()
+
+    def write_contents(self):
+        """
+        Write the available content from stdin and stderr where specified when the instance was created
+        :return:
+        """
+
+        def read_all_from_queue(queue):
+            res = b''
+            size = queue.qsize()
+            while size != 0:
+                res += queue.get_nowait()
+                size -= 1
+            return res
+
+        stderr_contents = read_all_from_queue(self._stderr_queue)
+        if stderr_contents:
+            self._write_to_stderr(stderr_contents.decode())
+
+        stdout_contents = read_all_from_queue(self._stdout_queue)
+        if stdout_contents:
+            contents = stdout_contents.decode()
+            # if there is input request, make output and then
+            # ask frontend for input
+            start = contents.find(self.__class__.inputRequest)
+            if(start >= 0):
+                contents = contents.replace(self.__class__.inputRequest, '')
+                if(len(contents) > 0):
+                    self._write_to_stdout(contents)
+                readLine = ""
+                while(len(readLine) == 0):
+                    readLine = self._read_from_stdin()
+                # need to add newline since it is not captured by frontend
+                readLine += "\n"
+                self.stdin.write(readLine.encode())
+            else:
+                self._write_to_stdout(contents)
 
 
 class CKernel(Kernel):
@@ -10,19 +91,42 @@ class CKernel(Kernel):
     language = 'c'
     language_version = 'C11'
     language_info = {'name': 'c',
-                     'mimetype': 'text/plain',
-                     'file_extension': 'c'}
+                     'mimetype': 'text/x-csrc',
+                     'file_extension': '.c'}
     banner = "C kernel.\n" \
              "Uses gcc, compiles in C11, and creates source code files and executables in temporary folder.\n"
 
+    main_head = "#include <stdio.h>\n" \
+            "#include <math.h>\n" \
+            "int main(){\n"
+
+    main_foot = "\nreturn 0;\n}"
+
     def __init__(self, *args, **kwargs):
         super(CKernel, self).__init__(*args, **kwargs)
+        self._allow_stdin = True
+        self.readOnlyFileSystem = False
+        self.bufferedOutput = True
+        self.linkMaths = True # always link math library
+        self.wAll = True # show all warnings by default
+        self.wError = False # but keep comipiling for warnings
+        self.standard = "c11" # default standard if none is specified
         self.files = []
+        mastertemp = tempfile.mkstemp(suffix='.out')
+        os.close(mastertemp[0])
+        self.master_path = mastertemp[1]
+        self.resDir = path.join(path.dirname(path.realpath(__file__)), 'resources')
+        filepath = path.join(self.resDir, 'master.c')
+        subprocess.call(['gcc', filepath, '-std=c11', '-rdynamic', '-ldl', '-o', self.master_path])
 
     def cleanup_files(self):
         """Remove all the temporary files created by the kernel"""
+        # keep the list of files create in case there is an exception
+        # before they can be deleted as usual
         for file in self.files:
-            os.remove(file)
+            if(os.path.exists(file)):
+                os.remove(file)
+        os.remove(self.master_path)
 
     def new_temp_file(self, **kwargs):
         """Create a new temp file to be deleted when the kernel shuts down"""
@@ -33,50 +137,138 @@ class CKernel(Kernel):
         self.files.append(file.name)
         return file
 
-    @staticmethod
-    def execute_command(cmd):
-        """Execute a command and returns the return code, stdout and stderr"""
-        p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        stdout, stderr = p.communicate()
-        return p.returncode, stdout.decode('utf-8'), stderr.decode('utf-8')
+    def _write_to_stdout(self, contents):
+        self.send_response(self.iopub_socket, 'stream', {'name': 'stdout', 'text': contents})
 
-    @staticmethod
-    def compile_with_gcc(source_filename, binary_filename):
-        args = ['gcc', source_filename, '-std=c11', '-o', binary_filename]
-        return CKernel.execute_command(args)
+    def _write_to_stderr(self, contents):
+        self.send_response(self.iopub_socket, 'stream', {'name': 'stderr', 'text': contents})
+
+    def _read_from_stdin(self):
+        return self.raw_input()
+
+    def create_jupyter_subprocess(self, cmd):
+        return RealTimeSubprocess(cmd,
+                                  self._write_to_stdout,
+                                  self._write_to_stderr,
+                                  self._read_from_stdin)
+
+    def compile_with_gcc(self, source_filename, binary_filename, cflags=None, ldflags=None):
+        cflags = ['-pedantic', '-fPIC', '-shared', '-rdynamic'] + cflags
+        if self.linkMaths:
+            cflags = cflags + ['-lm']
+        if self.wError:
+            cflags = cflags + ['-Werror']
+        if self.wAll:
+            cflags = cflags + ['-Wall']
+        if self.readOnlyFileSystem:
+            cflags = ['-DREAD_ONLY_FILE_SYSTEM'] + cflags
+        if self.bufferedOutput:
+            cflags = ['-DBUFFERED_OUTPUT'] + cflags
+        args = ['gcc', source_filename] + cflags + ['-o', binary_filename] + ldflags
+        return self.create_jupyter_subprocess(args)
+
+    def _filter_magics(self, code):
+
+        magics = {'cflags': [],
+                  'ldflags': [],
+                  'args': []}
+
+        actualCode = ''
+
+        for line in code.splitlines():
+            if line.startswith('//%'):
+                magicSplit = line[3:].split(":", 2)
+                if(len(magicSplit) < 2):
+                    self._write_to_stderr("[C kernel] Magic line starting with '//%' is missing a semicolon, ignoring.")
+                    continue
+
+                key, value = magicSplit
+                key = key.strip().lower()
+
+                if key in ['ldflags', 'cflags']:
+                    for flag in value.split():
+                        magics[key] += [flag]
+                elif key == "args":
+                    # Split arguments respecting quotes
+                    for argument in re.findall(r'(?:[^\s,"]|"(?:\\.|[^"])*")+', value):
+                        magics['args'] += [argument.strip('"')]
+
+                # always add empty line, so line numbers don't change
+                actualCode += '\n'
+
+            # keep lines which did not contain magics
+            else:
+                actualCode += line + '\n'
+
+        # add default standard if cflags does not contain one
+        if not any(item.startswith('-std=') for item in magics["cflags"]):
+            magics["cflags"] += ["-std=" + self.standard]
+
+        return magics, actualCode
+
+    # check whether int main() is specified, if not add it around the code
+    # also add common magics like -lm
+    def _add_main(self, magics, code):
+        # remove comments
+        tmpCode = re.sub(r"//.*", "", code)
+        tmpCode = re.sub(r"/\*.*?\*/", "", tmpCode, flags=re.M|re.S)
+
+        x = re.search(r"int\s+main\s*\(", tmpCode)
+
+        if not x:
+            code = self.main_head + code + self.main_foot
+            magics['cflags'] += ['-lm']
+
+        return magics, code
 
     def do_execute(self, code, silent, store_history=True,
-                   user_expressions=None, allow_stdin=False):
+                   user_expressions=None, allow_stdin=True):
+
+        magics, code = self._filter_magics(code)
+
+        magics, code = self._add_main(magics, code)
+
+        # replace stdio with wrapped version
+        headerDir = "\"" + self.resDir + "/stdio_wrap.h" + "\""
+        code = code.replace("<stdio.h>", headerDir)
+        code = code.replace("\"stdio.h\"", headerDir)
 
-        retcode, stdout, stderr = None, '', ''
         with self.new_temp_file(suffix='.c') as source_file:
             source_file.write(code)
             source_file.flush()
             with self.new_temp_file(suffix='.out') as binary_file:
-                retcode, stdout, stderr = self.compile_with_gcc(source_file.name, binary_file.name)
-                if retcode != 0:
-                    stderr += "[C kernel] GCC exited with code {}, the executable will not be executed".format(retcode)
-                self.log.info("GCC return code: {}".format(retcode))
-                self.log.info("GCC stdout: {}".format(stdout))
-                self.log.info("GCC stderr: {}".format(stderr))
+                p = self.compile_with_gcc(source_file.name, binary_file.name, magics['cflags'], magics['ldflags'])
+                while p.poll() is None:
+                    p.write_contents()
+                p.write_contents()
+                if p.returncode != 0:  # Compilation failed
+                    self._write_to_stderr(
+                            "[C kernel] GCC exited with code {}, the executable will not be executed".format(
+                                    p.returncode))
 
-        if retcode == 0:  # If the compilation succeeded
-            retcode, out, err = CKernel.execute_command([binary_file.name])
-            if retcode != 0:
-                stderr += "[C kernel] Executable exited with code {}".format(retcode)
-            self.log.info("Executable retcode: {}".format(retcode))
-            self.log.info("Executable stdout: {}".format(out))
-            self.log.info("Executable stderr: {}".format(err))
-            stdout += out
-            stderr += err
-        else:
-            self.log.info('Compilation failed, the program will not be executed')
+                    # delete source files before exit
+                    os.remove(source_file.name)
+                    os.remove(binary_file.name)
 
-        if not silent:
-            stream_content = {'name': 'stderr', 'text': stderr}
-            self.send_response(self.iopub_socket, 'stream', stream_content)
-            stream_content = {'name': 'stdout', 'text': stdout}
-            self.send_response(self.iopub_socket, 'stream', stream_content)
+                    return {'status': 'ok', 'execution_count': self.execution_count, 'payload': [],
+                            'user_expressions': {}}
+
+        p = self.create_jupyter_subprocess([self.master_path, binary_file.name] + magics['args'])
+        while p.poll() is None:
+            p.write_contents()
+
+        # wait for threads to finish, so output is always shown
+        p._stdout_thread.join()
+        p._stderr_thread.join()
+
+        p.write_contents()
+
+        # now remove the files we have just created
+        os.remove(source_file.name)
+        os.remove(binary_file.name)
+
+        if p.returncode != 0:
+            self._write_to_stderr("[C kernel] Executable exited with code {}".format(p.returncode))
         return {'status': 'ok', 'execution_count': self.execution_count, 'payload': [], 'user_expressions': {}}
 
     def do_shutdown(self, restart):

jupyter_c_kernel/resources/master.c

@@ -0,0 +1,31 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <dlfcn.h>
+
+typedef int (*main_t)(int, char **, char **);
+
+int main(int argc, char **argv, char **envp)
+{
+    char *error = NULL;
+
+    setbuf(stdout, NULL);
+    setbuf(stderr, NULL);
+    if (argc < 2) {
+        fprintf(stderr, "USAGE: %s PROGRAM\nWhere PROGRAM is the user's program to supervise\n", argv[0]);
+        return EXIT_FAILURE;
+    }
+    void *userhandle = dlopen(argv[1], RTLD_LAZY);
+    if (userhandle == NULL) {
+        fprintf(stderr, "%s: %s\n", argv[0], dlerror());
+        return EXIT_FAILURE;
+    }
+    dlerror();
+    main_t usermain = dlsym(userhandle, "main");
+    if ((error = dlerror()) != NULL) {
+        fprintf(stderr, "%s: %s\n", argv[0], error);
+        return EXIT_FAILURE;
+    }
+
+    /* Call Users main, but make master.c invisible by removing first argument */
+    return usermain(argc-1, argv+1, envp);
+}

jupyter_c_kernel/resources/stdio_wrap.h

@@ -0,0 +1,329 @@
+#ifndef STDIO_WRAP_H
+#define STDIO_WRAP_H
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <string.h>
+#include <stdlib.h>
+#include <ctype.h>
+
+/* Figure out used C standard.
+  __STDC_VERSION__ is not always defined until C99.
+  If it is not defined, set standard to C89.
+  It is safest to set it by hand, to make sure */
+#ifdef __STDC_VERSION__
+#if __STDC_VERSION__ <= 199409L
+#define C89_SUPPORT
+#endif /* __STDC_VERSION__ <= 199409L */
+#else /* __STDC_VERSION__ */
+#define C89_SUPPORT
+#endif /* __STDC_VERSION__ */
+
+/* output functions to replicate terminal behaviour */
+#ifdef BUFFERED_OUTPUT
+/* buffer for all output */
+/* TODO allocate this dynamically */
+static char outputBuff[1<<10] = "";
+static char attachedOutputFlush = 0;
+
+void flush_all_output() {
+  printf("%s", outputBuff);
+  fflush(stdout);
+  outputBuff[0] = '\0';
+}
+
+/* Flush all output on exit */
+void attachOutputFlush() {
+  if(attachedOutputFlush == 0){
+    int error = atexit(flush_all_output);
+    if(error != 0) {
+      fprintf(stderr, "ERROR: Could not set exit function! Error %d\n", error);
+    }
+    attachedOutputFlush = 1;
+  }
+}
+
+/* this function is called to check whether there
+  is a '\n' in the output that should be flushed */
+void flush_until_newline() {
+  long i = 0;
+  long length = strlen(outputBuff);
+  for(; i < length; ++i) {
+    if(outputBuff[i] == '\n') {
+      char *printBuff = malloc(i+2);
+      strncpy(printBuff, outputBuff, i+1);
+      printBuff[i+1] = '\0';
+      printf("%s", printBuff);
+      free(printBuff);
+      /* now remove the printed string from the buffer
+        and start again */
+      {
+        long a = 0;
+        ++i;
+        /* +1 to include \0 */
+        for(; i < length + 1; ++a, ++i) {
+          outputBuff[a] = outputBuff[i];
+        }
+        i = 0;
+        length = strlen(outputBuff);
+      }
+    }
+  }
+}
+
+/* for printf, print all to a string.
+  Then cycle through all chars and see if \n is
+  written. If there is one, flush the output, otherwise
+  write to buffer */
+int printf_wrap(const char *format, ...) {
+  /* append output to buffer */
+  va_list arglist;
+  int result;
+  va_start( arglist, format );
+  result = vsprintf(outputBuff + strlen(outputBuff), format, arglist);
+  va_end( arglist );
+
+  /* Now flush if there is a reason to */
+  flush_until_newline();
+
+  attachOutputFlush();
+
+  return result;
+}
+
+int putchar_wrap(int c) {
+  long length = strlen(outputBuff);
+  outputBuff[length] = (char)c;
+  outputBuff[length+1] = '\0';
+  if(c == '\n') {
+    flush_until_newline();
+  }
+
+  attachOutputFlush();
+
+  return c;
+}
+
+int fflush_wrap(FILE* stream) {
+  if(stream == stdout) {
+    flush_all_output();
+  }
+  return fflush(stream);
+}
+
+int fclose_wrap(FILE* stream) {
+  if(stream == stdout) {
+    flush_all_output();
+  }
+  return fclose(stream);
+}
+#endif /* BUFFERED_OUTPUT */
+
+/* Need input buffer to know whether we need another input request */
+/* TODO allocate this dynamically */
+static char inputBuff[1<<10] = "";
+static long scanf_wrap_number_read = 0;
+
+/* read remaining input into buffer so it can be used in next call */
+void readIntoBuffer(void) {
+  long length = strlen(inputBuff);
+  char nextChar = 0;
+  while((nextChar = getchar()) != '\n' && nextChar != EOF){
+    inputBuff[length++] = nextChar;
+  }
+  inputBuff[length++] = '\n';
+  inputBuff[length] = '\0';
+}
+
+/* check whether input request is needed */
+char checkInputRequest(void) {
+  const long length = strlen(inputBuff);
+  long i = 0;
+  for(; i < length && isspace(inputBuff[i]); ++i);
+  return i == length;
+}
+
+/* Define the input functions to overload the old ones */
+/* Wrapping of scanf depends on standard */
+#ifdef C89_SUPPORT
+/* Need to define vscanf for c89.
+  TODO: This is a bit risky, since the underlying glibc does not
+  have to include this if it is old. If it does not, linking will fail.
+  The robust way would be readin via sscanf. */
+
+/* Read formatted input from stdin into argument list ARG.
+
+   This function is a possible cancellation point and therefore not
+   marked with __THROW.  */
+   extern int vsscanf (const char *__restrict __s,
+                       const char *__restrict __format, _G_va_list __arg)
+        __THROW __attribute__ ((__format__ (__scanf__, 2, 0)));
+
+  /* replace all % with %* to suppress read in and do test run */
+  long find_scanf_length(const char *format) {
+    const long length = strlen(format);
+    /* allow for maximum of 50 format specifiers */
+    char *formatString = malloc(length + 53);
+    long index = 0;
+    long formatIndex = 0;
+    for(; index < length; ++index, ++formatIndex) {
+      formatString[formatIndex] = format[index];
+      if(format[index] == '%' &&
+        (index + 1 < length && format[index + 1] != '%')) {
+        formatString[++formatIndex] = '*';
+      }
+    }
+    /* add number readin */
+    formatString[formatIndex++] = '%';
+    formatString[formatIndex++] = 'n';
+    formatString[formatIndex] = '\0';
+
+    /* now run and record how many characters were read */
+    {
+      int readLength = 0;
+      sscanf(inputBuff, formatString, &readLength);
+      free(formatString);
+
+      return readLength;
+    }
+  }
+#endif /* C89_SUPPORT */
+
+int scanf_wrap(const char *format, ...) {
+  char doRequest = checkInputRequest();
+  char *formatString = 0;
+
+  if(doRequest) {
+#ifdef BUFFERED_OUTPUT
+    flush_all_output();
+#endif
+    printf("<inputRequest>");
+    fflush(stdout);
+    /* read everything from stdin into buffer */
+    readIntoBuffer();
+  }
+
+  /* add %n to format string to get number of written chars */
+  {
+    const long length = strlen(format);
+    formatString = malloc(length + 3);
+    strcpy(formatString, format);
+#ifndef C89_SUPPORT
+    formatString[length] = '%';
+    formatString[length + 1] = 'n';
+    formatString[length + 2] = '\0';
+#else /* C89_SUPPORT */
+    formatString[length] = '\0';
+    /* In C89 we need to find how far scanf will read, by hand */
+    scanf_wrap_number_read = find_scanf_length(format);
+#endif /* C89_SUPPORT */
+  }
+
+  {
+    va_list arglist;
+    int result;
+    va_start(arglist, format);
+    result = vsscanf(inputBuff, formatString, arglist);
+    va_end(arglist);
+
+    /* now move inputBuff up */
+    {
+      const long length = strlen(inputBuff);
+      long index = scanf_wrap_number_read;
+      long a = 0;
+      /* +1 to include \0 */
+      for(; index < length + 1; ++a, ++index) {
+        inputBuff[a] = inputBuff[index];
+      }
+    }
+
+    free(formatString);
+    return result;
+  }
+}
+
+int getchar_wrap(void){
+  /* check if there is still something in the input buffer*/
+  char input = 0;
+  long length = strlen(inputBuff);
+  if(length <= 0) {
+#ifdef BUFFERED_OUTPUT
+    flush_all_output();
+#endif
+    printf("<inputRequest>");
+    fflush(stdout);
+
+    readIntoBuffer();
+  }
+
+  input = inputBuff[0];
+  {
+    long i = 1;
+    long length = strlen(inputBuff) + 1;
+    /* shift all chars one to the left */
+    for(; i < length; ++i){
+      inputBuff[i-1] = inputBuff[i];
+      if(inputBuff[i] == '\0') {
+        break;
+      }
+    }
+  }
+
+  return input;
+}
+
+/* Replace all the necessary input functions
+  depending on the language version used */
+#ifndef C89_SUPPORT
+/* Need double hashes in case there are no __VA_ARGS__*/
+#define scanf(format, ...) scanf_wrap(format, ##__VA_ARGS__, &scanf_wrap_number_read)
+#else /* C89_SUPPORT */
+/* Since there are no variadic macros in C89, this is the only way
+  although it is horrible */
+#define scanf scanf_wrap
+#endif /* C89_SUPPORT */
+
+#define getchar() getchar_wrap()
+
+/* Output defines */
+#ifdef BUFFERED_OUTPUT
+#define printf printf_wrap
+#define putchar putchar_wrap
+#define fflush fflush_wrap
+#define fclose fclose_wrap
+#endif /* BUFFERED_OUTPUT */
+
+/* Replace FILE write operations for read-only systems */
+#ifdef READ_ONLY_FILE_SYSTEM
+
+/* Define wrapping functions */
+/* Output that the fopen succeeded and return some valid pointer */
+FILE *fopen_wrap(const char *filename, const char *modes) {
+  static long stream = 0x1FFFF0000;
+#ifdef SHOW_FILE_IO_VERBOSE
+  printf("\x01b[42m");
+  printf("\"%s\" opened in mode \"%s\"\n", filename, modes);
+  printf("\x01b[0m");
+#endif /* SHOW_FILE_IO_VERBOSE */
+  return (FILE*)stream++;
+}
+
+int fprintf_wrap(FILE* stream, const char* format, ...) {
+  printf("\x01b[42m");
+  printf("%p:", stream);
+  printf("\x01b[0m");
+  va_list arglist;
+  va_start( arglist, format );
+  int result = vprintf(format, arglist);
+  va_end( arglist );
+  return result;
+}
+
+/* Replace all the necessary input functions */
+#define fopen(file, mode) fopen_wrap(file, mode)
+
+#define fprintf(stream, format, ...) fprintf_wrap(stream, format, ##__VA_ARGS__)
+
+#endif  /* READ_ONLY_FILE_SYSTEM */
+
+#endif /* STDIO_WRAP_H */

setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md

setup.py

@@ -1,10 +1,18 @@
-from distutils.core import setup
+from setuptools import setup
 
 setup(name='jupyter_c_kernel',
-      version='1.0.0',
+      version='1.2.1',
       description='Minimalistic C kernel for Jupyter',
       author='Brendan Rius',
       author_email='ping@brendan-rius.com',
+      license='MIT',
+      classifiers=[
+          'License :: OSI Approved :: MIT License',
+      ],
+      url='https://github.com/brendan-rius/jupyter-c-kernel/',
+      download_url='https://github.com/brendan-rius/jupyter-c-kernel/tarball/1.2.1',
       packages=['jupyter_c_kernel'],
-      keywords=['jupyter', 'kernel', 'c']
+      scripts=['jupyter_c_kernel/install_c_kernel'],
+      keywords=['jupyter', 'notebook', 'kernel', 'c'],
+      include_package_data=True
       )