static void
_cleanup_editlineobject(EditLineObject *self)
{
    /* mop up libedit */
    if (self->el)
	el_end(self->el);
    if (self->tok)
	tok_end(self->tok);
    if (self->hist)
	history_end(self->hist);

    /* tidy up the allocated bits */
    if (self->name)
	PyMem_RawFree(self->name);
    if (self->prompt)
	PyMem_RawFree(self->prompt);
    if (self->rprompt)
	PyMem_RawFree(self->rprompt);
    if (self->buffer)
	PyMem_RawFree(self->buffer);
    
    /* manage file-handles? */
    if (self->fin)
	fclose(self->fin);
    if (self->fout)
	fclose(self->fout);
    if (self->ferr)
	fclose(self->ferr);

    /* release my ownership of the I/O refs */
    Py_DECREF(self->pyin);
    Py_DECREF(self->pyout);
    Py_DECREF(self->pyerr);
}

int nacl_main(int argc, char **argv) {
    if (nacl_startup_untar(argv[0], DATA_FILE, "/"))
      return -1;

    wchar_t **argv_copy;
    /* We need a second copy, as Python might modify the first one. */
    wchar_t **argv_copy2;
    int i, res;
    char *oldloc;
#ifdef __FreeBSD__
    fp_except_t m;
#endif

    argv_copy = (wchar_t **)PyMem_RawMalloc(sizeof(wchar_t*) * (argc+1));
    argv_copy2 = (wchar_t **)PyMem_RawMalloc(sizeof(wchar_t*) * (argc+1));
    if (!argv_copy || !argv_copy2) {
        fprintf(stderr, "out of memory\n");
        return 1;
    }

    /* 754 requires that FP exceptions run in "no stop" mode by default,
     * and until C vendors implement C99's ways to control FP exceptions,
     * Python requires non-stop mode.  Alas, some platforms enable FP
     * exceptions by default.  Here we disable them.
     */
#ifdef __FreeBSD__
    m = fpgetmask();
    fpsetmask(m & ~FP_X_OFL);
#endif

    oldloc = _PyMem_RawStrdup(setlocale(LC_ALL, NULL));
    if (!oldloc) {
        fprintf(stderr, "out of memory\n");
        return 1;
    }

    setlocale(LC_ALL, "");
    for (i = 0; i < argc; i++) {
        argv_copy[i] = _Py_char2wchar(argv[i], NULL);
        if (!argv_copy[i]) {
            PyMem_RawFree(oldloc);
            fprintf(stderr, "Fatal Python error: "
                            "unable to decode the command line argument #%i\n",
                            i + 1);
            return 1;
        }
        argv_copy2[i] = argv_copy[i];
    }
    argv_copy2[argc] = argv_copy[argc] = NULL;

    setlocale(LC_ALL, oldloc);
    PyMem_RawFree(oldloc);
    res = Py_Main(argc, argv_copy);
    for (i = 0; i < argc; i++) {
        PyMem_RawFree(argv_copy2[i]);
    }
    PyMem_RawFree(argv_copy);
    PyMem_RawFree(argv_copy2);
    return res;
}

wchar_t*
_Py_wrealpath(const wchar_t *path,
              wchar_t *resolved_path, size_t resolved_path_size)
{
    char *cpath;
    char cresolved_path[MAXPATHLEN];
    wchar_t *wresolved_path;
    char *res;
    size_t r;
    cpath = _Py_wchar2char(path, NULL);
    if (cpath == NULL) {
        errno = EINVAL;
        return NULL;
    }
    res = realpath(cpath, cresolved_path);
    PyMem_Free(cpath);
    if (res == NULL)
        return NULL;

    wresolved_path = _Py_char2wchar(cresolved_path, &r);
    if (wresolved_path == NULL) {
        errno = EINVAL;
        return NULL;
    }
    if (resolved_path_size <= r) {
        PyMem_RawFree(wresolved_path);
        errno = EINVAL;
        return NULL;
    }
    wcsncpy(resolved_path, wresolved_path, resolved_path_size);
    PyMem_RawFree(wresolved_path);
    return resolved_path;
}

wchar_t*
_Py_wgetcwd(wchar_t *buf, size_t size)
{
#ifdef MS_WINDOWS
    int isize = (int)Py_MIN(size, INT_MAX);
    return _wgetcwd(buf, isize);
#else
    char fname[MAXPATHLEN];
    wchar_t *wname;
    size_t len;

    if (getcwd(fname, Py_ARRAY_LENGTH(fname)) == NULL)
        return NULL;
    wname = _Py_char2wchar(fname, &len);
    if (wname == NULL)
        return NULL;
    if (size <= len) {
        PyMem_RawFree(wname);
        return NULL;
    }
    wcsncpy(buf, wname, size);
    PyMem_RawFree(wname);
    return buf;
#endif
}

static void
calculate_free(PyCalculatePath *calculate)
{
    PyMem_RawFree(calculate->pythonpath);
    PyMem_RawFree(calculate->prefix);
    PyMem_RawFree(calculate->exec_prefix);
    PyMem_RawFree(calculate->lib_python);
    PyMem_RawFree(calculate->path_env);
}

PyObject* getFileData(int argc, char *argv[])
{
    PyObject *BioModule = PyImport_ImportModule("Bio");
    const char *filename, *filetype, *pycmdToRun;
    filename = (const char *)PyUnicode_DecodeFSDefault(argv[1]);
    filetype = (const char *)PyUnicode_DecodeFSDefault(argv[2]);
    std::string cmdToRun = "import Bio\nBio.SeqIO.parse(";
    cmdToRun = cmdToRun + filename + std::string(",") + filetype;
    pycmdToRun = cmdToRun.c_str();

    wchar_t *program = Py_DecodeLocale(argv[0], NULL);
    if (program == NULL) {
        fprintf(stderr, "Fatal error: cannot decode argv[0]\n");
        exit(1);
    }
    
    Py_SetProgramName(program);  /* optional but recommended */
    Py_Initialize();
    PyObject* filedata;
    filedata = PyRun_String(pycmdToRun, 0, NULL, NULL);
    Py_DECREF(filename);
    Py_DECREF(filetype);
    Py_Finalize();
    PyMem_RawFree(program);

    return filedata;
}

/*
 * Delete all thread states except the one passed as argument.
 * Note that, if there is a current thread state, it *must* be the one
 * passed as argument.  Also, this won't touch any other interpreters
 * than the current one, since we don't know which thread state should
 * be kept in those other interpreteres.
 */
void
_PyThreadState_DeleteExcept(PyThreadState *tstate)
{
    PyInterpreterState *interp = tstate->interp;
    PyThreadState *p, *next, *garbage;
    HEAD_LOCK();
    /* Remove all thread states, except tstate, from the linked list of
       thread states.  This will allow calling PyThreadState_Clear()
       without holding the lock. */
    garbage = interp->tstate_head;
    if (garbage == tstate)
        garbage = tstate->next;
    if (tstate->prev)
        tstate->prev->next = tstate->next;
    if (tstate->next)
        tstate->next->prev = tstate->prev;
    tstate->prev = tstate->next = NULL;
    interp->tstate_head = tstate;
    HEAD_UNLOCK();
    /* Clear and deallocate all stale thread states.  Even if this
       executes Python code, we should be safe since it executes
       in the current thread, not one of the stale threads. */
    for (p = garbage; p; p = next) {
        next = p->next;
        PyThreadState_Clear(p);
        PyMem_RawFree(p);
    }
}

/* Forget everything not associated with the current thread id.
 * This function is called from PyOS_AfterFork().  It is necessary
 * because other thread ids which were in use at the time of the fork
 * may be reused for new threads created in the forked process.
 */
void
PyThread_ReInitTLS(void)
{
    long id = PyThread_get_thread_ident();
    struct key *p, **q;

    if (!keymutex)
        return;

    /* As with interpreter_lock in PyEval_ReInitThreads()
       we just create a new lock without freeing the old one */
    keymutex = PyThread_allocate_lock();

    /* Delete all keys which do not match the current thread id */
    q = &keyhead;
    while ((p = *q) != NULL) {
        if (p->id != id) {
            *q = p->next;
            PyMem_RawFree((void *)p);
            /* NB This does *not* free p->value! */
        }
        else
            q = &p->next;
    }
}

static PyObject *
overlapped_RegisterWaitWithQueue(PyObject *self, PyObject *args)
{
    HANDLE NewWaitObject;
    HANDLE Object;
    ULONG Milliseconds;
    struct PostCallbackData data, *pdata;

    if (!PyArg_ParseTuple(args, F_HANDLE F_HANDLE F_POINTER F_DWORD,
                          &Object,
                          &data.CompletionPort,
                          &data.Overlapped,
                          &Milliseconds))
        return NULL;

    /* Use PyMem_RawMalloc() rather than PyMem_Malloc(), since
       PostToQueueCallback() will call PyMem_Free() from a new C thread
       which doesn't hold the GIL. */
    pdata = PyMem_RawMalloc(sizeof(struct PostCallbackData));
    if (pdata == NULL)
        return SetFromWindowsErr(0);

    *pdata = data;

    if (!RegisterWaitForSingleObject(
            &NewWaitObject, Object, (WAITORTIMERCALLBACK)PostToQueueCallback,
            pdata, Milliseconds,
            WT_EXECUTEINWAITTHREAD | WT_EXECUTEONLYONCE))
    {
        PyMem_RawFree(pdata);
        return SetFromWindowsErr(0);
    }

    return Py_BuildValue(F_HANDLE, NewWaitObject);
}

void
PyInterpreterState_Delete(PyInterpreterState *interp)
{
    PyInterpreterState **p;
    zapthreads(interp);
    HEAD_LOCK();
    for (p = &_PyRuntime.interpreters.head; ; p = &(*p)->next) {
        if (*p == NULL)
            Py_FatalError(
                "PyInterpreterState_Delete: invalid interp");
        if (*p == interp)
            break;
    }
    if (interp->tstate_head != NULL)
        Py_FatalError("PyInterpreterState_Delete: remaining threads");
    *p = interp->next;
    if (_PyRuntime.interpreters.main == interp) {
        _PyRuntime.interpreters.main = NULL;
        if (_PyRuntime.interpreters.head != NULL)
            Py_FatalError("PyInterpreterState_Delete: remaining subinterpreters");
    }
    HEAD_UNLOCK();
    if (interp->id_mutex != NULL) {
        PyThread_free_lock(interp->id_mutex);
    }
    if (interp->ceval.pending.lock != NULL) {
        PyThread_free_lock(interp->ceval.pending.lock);
    }
    PyMem_RawFree(interp);
}

int
Py_SetStandardStreamEncoding(const char *encoding, const char *errors)
{
    if (Py_IsInitialized()) {
        /* This is too late to have any effect */
        return -1;
    }
    /* Can't call PyErr_NoMemory() on errors, as Python hasn't been
     * initialised yet.
     *
     * However, the raw memory allocators are initialised appropriately
     * as C static variables, so _PyMem_RawStrdup is OK even though
     * Py_Initialize hasn't been called yet.
     */
    if (encoding) {
        _Py_StandardStreamEncoding = _PyMem_RawStrdup(encoding);
        if (!_Py_StandardStreamEncoding) {
            return -2;
        }
    }
    if (errors) {
        _Py_StandardStreamErrors = _PyMem_RawStrdup(errors);
        if (!_Py_StandardStreamErrors) {
            if (_Py_StandardStreamEncoding) {
                PyMem_RawFree(_Py_StandardStreamEncoding);
            }
            return -3;
        }
    }
    return 0;
}

/*
 * Delete all interpreter states except the main interpreter.  If there
 * is a current interpreter state, it *must* be the main interpreter.
 */
void
_PyInterpreterState_DeleteExceptMain()
{
    PyThreadState *tstate = PyThreadState_Swap(NULL);
    if (tstate != NULL && tstate->interp != _PyRuntime.interpreters.main) {
        Py_FatalError("PyInterpreterState_DeleteExceptMain: not main interpreter");
    }

    HEAD_LOCK();
    PyInterpreterState *interp = _PyRuntime.interpreters.head;
    _PyRuntime.interpreters.head = NULL;
    while (interp != NULL) {
        if (interp == _PyRuntime.interpreters.main) {
            _PyRuntime.interpreters.main->next = NULL;
            _PyRuntime.interpreters.head = interp;
            interp = interp->next;
            continue;
        }

        PyInterpreterState_Clear(interp);  // XXX must activate?
        zapthreads(interp);
        if (interp->id_mutex != NULL) {
            PyThread_free_lock(interp->id_mutex);
        }
        PyInterpreterState *prev_interp = interp;
        interp = interp->next;
        PyMem_RawFree(prev_interp);
    }
    HEAD_UNLOCK();

    if (_PyRuntime.interpreters.head == NULL) {
        Py_FatalError("PyInterpreterState_DeleteExceptMain: missing main");
    }
    PyThreadState_Swap(tstate);
}

void
PyInterpreterState_Delete(PyInterpreterState *interp)
{
    PyInterpreterState **p;
    zapthreads(interp);
    HEAD_LOCK();
    for (p = &interp_head; ; p = &(*p)->next) {
        if (*p == NULL)
            Py_FatalError(
                "PyInterpreterState_Delete: invalid interp");
        if (*p == interp)
            break;
    }
    if (interp->tstate_head != NULL)
        Py_FatalError("PyInterpreterState_Delete: remaining threads");
    *p = interp->next;
    HEAD_UNLOCK();
    PyMem_RawFree(interp);
#ifdef WITH_THREAD
    if (interp_head == NULL && head_mutex != NULL) {
        PyThread_free_lock(head_mutex);
        head_mutex = NULL;
    }
#endif
}

static wchar_t* Py_DecodeLocale(const char* arg, size_t*) {
    size_t argsize = mbstowcs(NULL, arg, 0);
    if (argsize == (size_t)-1) {
        return NULL;
    }
    if (argsize == PY_SSIZE_T_MAX) {
        return NULL;
    }
    if (argsize > PY_SSIZE_T_MAX/sizeof(wchar_t)) {
        return NULL;
    }
    wchar_t *res = (wchar_t *)PyMem_RawMalloc(argsize*sizeof(wchar_t));
    if (!res) {
        return NULL;
    }
    size_t count = mbstowcs(res, arg, argsize);
    if (count != (size_t)-1) {
        wchar_t *tmp;
        for (tmp = res; *tmp != 0 && !Py_UNICODE_IS_SURROGATE(*tmp); tmp++) {
        }
        if (*tmp == 0) {
            return res;
        }
    }
    PyMem_RawFree(res);
    return NULL;
}

static int
elObj_rprompt_setter(EditLineObject *self, PyObject *value, void *closure)
{
    int rv = 0;
    int n;
    char *new_rprompt;
    const char *encoded_c;
    PyObject *encoded;
    
    if (value == NULL) {
        PyErr_SetString(PyExc_TypeError, "Cannot delete the rprompt attribute");
        return -1;
    }

    if (! PyUnicode_Check(value)) {
        PyErr_SetString(PyExc_TypeError,
                        "The rprompt attribute value must be a string");
        return -1;
    }

    /* it is stored as a C string */
    encoded = encode(value);
    if (encoded == NULL) {
        PyErr_SetString(PyExc_ValueError,
                        "The rprompt attribute could not be encoded");
        return -1;
    }

    /* get it as a c-string */
    encoded_c = PyBytes_AS_STRING(encoded);
    n = strlen(encoded_c);

    /* create a RawMalloc'd buffer */
    new_rprompt = PyMem_RawMalloc(n+1);
    if (new_rprompt == NULL) {
	Py_DECREF(encoded);
	PyErr_NoMemory();
	return -1;
    }

    /* Copy the malloc'ed buffer into a PyMem_Malloc'ed one. */
    strncpy(new_rprompt, encoded_c, n);
    new_rprompt[n] = '\0';

    /* release the previous one if it was assigned */
    if (self->rprompt)
	PyMem_RawFree(self->rprompt);

    /* make this the active one */
    self->rprompt = new_rprompt;

    /*
     * REFs:  only manage 'enc' to ensure it gets removed.  We don't 'own'
     *        any of the others, so we just borrow the ref.
     */
    Py_DECREF(encoded);

    /* done */
    return rv;
}

/* Search for a prefix value in an environment file (pyvenv.cfg).
   If found, copy it into the provided buffer. */
int
_Py_FindEnvConfigValue(FILE *env_file, const wchar_t *key,
                       wchar_t *value, size_t value_size)
{
    int result = 0; /* meaning not found */
    char buffer[MAXPATHLEN*2+1];  /* allow extra for key, '=', etc. */

    fseek(env_file, 0, SEEK_SET);
    while (!feof(env_file)) {
        char * p = fgets(buffer, MAXPATHLEN*2, env_file);

        if (p == NULL) {
            break;
        }

        size_t n = strlen(p);
        if (p[n - 1] != '\n') {
            /* line has overflowed - bail */
            break;
        }
        if (p[0] == '#') {
            /* Comment - skip */
            continue;
        }

        wchar_t *tmpbuffer = _Py_DecodeUTF8_surrogateescape(buffer, n);
        if (tmpbuffer) {
            wchar_t * state;
            wchar_t * tok = wcstok(tmpbuffer, L" \t\r\n", &state);
            if ((tok != NULL) && !wcscmp(tok, key)) {
                tok = wcstok(NULL, L" \t", &state);
                if ((tok != NULL) && !wcscmp(tok, L"=")) {
                    tok = wcstok(NULL, L"\r\n", &state);
                    if (tok != NULL) {
                        wcsncpy(value, tok, MAXPATHLEN);
                        result = 1;
                        PyMem_RawFree(tmpbuffer);
                        break;
                    }
                }
            }
            PyMem_RawFree(tmpbuffer);
        }
    }
    return result;
}

static VOID CALLBACK
PostToQueueCallback(PVOID lpParameter, BOOL TimerOrWaitFired)
{
    struct PostCallbackData *p = (struct PostCallbackData*) lpParameter;

    PostQueuedCompletionStatus(p->CompletionPort, TimerOrWaitFired,
                               0, p->Overlapped);
    /* ignore possible error! */
    PyMem_RawFree(p);
}

static int
encode_ascii(const wchar_t *text, char **str,
             size_t *error_pos, const char **reason,
             int raw_malloc, int surrogateescape)
{
    char *result = NULL, *out;
    size_t len, i;
    wchar_t ch;

    len = wcslen(text);

    /* +1 for NULL byte */
    if (raw_malloc) {
        result = PyMem_RawMalloc(len + 1);
    }
    else {
        result = PyMem_Malloc(len + 1);
    }
    if (result == NULL) {
        return -1;
    }

    out = result;
    for (i=0; i<len; i++) {
        ch = text[i];

        if (ch <= 0x7f) {
            /* ASCII character */
            *out++ = (char)ch;
        }
        else if (surrogateescape && 0xdc80 <= ch && ch <= 0xdcff) {
            /* UTF-8b surrogate */
            *out++ = (char)(ch - 0xdc00);
        }
        else {
            if (raw_malloc) {
                PyMem_RawFree(result);
            }
            else {
                PyMem_Free(result);
            }
            if (error_pos != NULL) {
                *error_pos = i;
            }
            if (reason) {
                *reason = "encoding error";
            }
            return -2;
        }
    }
    *out = '\0';
    *str = result;
    return 0;
}

/* Get file status. Encode the path to the locale encoding. */
static int
_Py_wstat(const wchar_t* path, struct stat *buf)
{
    int err;
    char *fname;
    fname = _Py_EncodeLocaleRaw(path, NULL);
    if (fname == NULL) {
        errno = EINVAL;
        return -1;
    }
    err = stat(fname, buf);
    PyMem_RawFree(fname);
    return err;
}

int
_Py_wreadlink(const wchar_t *path, wchar_t *buf, size_t bufsiz)
{
    char *cpath;
    char cbuf[MAXPATHLEN];
    wchar_t *wbuf;
    int res;
    size_t r1;

    cpath = _Py_wchar2char(path, NULL);
    if (cpath == NULL) {
        errno = EINVAL;
        return -1;
    }
    res = (int)readlink(cpath, cbuf, Py_ARRAY_LENGTH(cbuf));
    PyMem_Free(cpath);
    if (res == -1)
        return -1;
    if (res == Py_ARRAY_LENGTH(cbuf)) {
        errno = EINVAL;
        return -1;
    }
    cbuf[res] = '\0'; /* buf will be null terminated */
    wbuf = _Py_char2wchar(cbuf, &r1);
    if (wbuf == NULL) {
        errno = EINVAL;
        return -1;
    }
    if (bufsiz <= r1) {
        PyMem_RawFree(wbuf);
        errno = EINVAL;
        return -1;
    }
    wcsncpy(buf, wbuf, bufsiz);
    PyMem_RawFree(wbuf);
    return (int)r1;
}