MLECO-2919: Restructuring to standardise HAL APIs

* LCD module component created (removed from individual
  platform packs).

* retarget.c moved out into its own component that wraps
  the uart module. It also have the native stub for
  GetLine => paved the way for removing data_acq module
  from profiles.

* shortened names for components' dir for npu and ta

* remove peripheral_memmap and peripheral_irqs headers
  from platform_drivers.h. There should be no need for
  these to be included in the top level now. These should
  be private headers.

* cmsis_device moved in as a component.

* Pyenv created by set_up_default_resource.py will also
  install packages that CMake's source generator needs.

TODO's:

* Remove timer from profiles (MLECO-3096)

Change-Id: I9d6ea2f4f291788f40a16ed507019563c8d7f205
diff --git a/source/hal/source/platform/mps3/source/timer_mps3.c b/source/hal/source/platform/mps3/source/timer_mps3.c
new file mode 100644
index 0000000..3511883
--- /dev/null
+++ b/source/hal/source/platform/mps3/source/timer_mps3.c
@@ -0,0 +1,193 @@
+/*
+ * Copyright (c) 2022 Arm Limited. All rights reserved.
+ * SPDX-License-Identifier: Apache-2.0
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#include "timer_mps3.h"
+
+#include "log_macros.h"
+#include "smm_mps3.h"   /* Memory map for MPS3. */
+
+static uint64_t cpu_cycle_count = 0;    /* 64-bit cpu cycle counter */
+
+/**
+ * @brief   Gets the system tick triggered cycle counter for the CPU.
+ * @return  64-bit counter value.
+ **/
+static uint64_t Get_SysTick_Cycle_Count(void);
+
+/**
+ * SysTick initialisation
+ */
+static int Init_SysTick(void);
+
+void timer_reset(void)
+{
+    MPS3_FPGAIO->CLK1HZ   = 0;
+    MPS3_FPGAIO->CLK100HZ = 0;
+    MPS3_FPGAIO->COUNTER  = 0;
+
+    if (0 != Init_SysTick()) {
+        printf_err("Failed to initialise system tick config\n");
+    }
+    debug("system tick config ready\n");
+}
+
+base_time_counter get_time_counter(void)
+{
+    base_time_counter t = {
+        .counter_1Hz        = MPS3_FPGAIO->CLK1HZ,
+        .counter_100Hz      = MPS3_FPGAIO->CLK100HZ,
+        .counter_fpga       = MPS3_FPGAIO->COUNTER,
+        .counter_systick    = Get_SysTick_Cycle_Count()
+    };
+    debug("Timestamp:\n");
+    debug("\tCounter 1 Hz:   %" PRIu32 "\n", t.counter_1Hz);
+    debug("\tCounter 100 Hz: %" PRIu32 "\n", t.counter_100Hz);
+    debug("\tCounter FPGA:   %" PRIu32 "\n", t.counter_fpga);
+    debug("\tCounter CPU:    %" PRIu64 "\n", t.counter_systick);
+    return t;
+}
+
+/**
+ * Please note, that there are no checks for overflow in this function => if
+ * the time elapsed has been big (in days) this could happen and is currently
+ * not handled.
+ **/
+uint32_t get_duration_milliseconds(base_time_counter *start,
+                                   base_time_counter *end)
+{
+    uint32_t time_elapsed = 0;
+    if (end->counter_100Hz > start->counter_100Hz) {
+        time_elapsed = (end->counter_100Hz - start->counter_100Hz) * 10;
+    } else {
+        time_elapsed = (end->counter_1Hz - start->counter_1Hz) * 1000 +
+            ((0xFFFFFFFF - start->counter_100Hz) + end->counter_100Hz + 1) * 10;
+    }
+
+    /* If the time elapsed is less than 100ms, use microseconds count to be
+     * more precise */
+    if (time_elapsed < 100) {
+        debug("Using the microsecond function instead..\n");
+        return get_duration_microseconds(start, end)/1000;
+    }
+
+    return time_elapsed;
+}
+
+/**
+ * Like the microsecond counterpart, this function could return wrong results when
+ * the counter (MAINCLK) overflows. There are no overflow counters available.
+ **/
+uint32_t get_duration_microseconds(base_time_counter *start,
+                                   base_time_counter *end)
+{
+    const int divisor = get_mps3_core_clock()/1000000;
+    uint32_t time_elapsed = 0;
+    if (end->counter_fpga > start->counter_fpga) {
+        time_elapsed = (end->counter_fpga - start->counter_fpga)/divisor;
+    } else {
+        time_elapsed = ((0xFFFFFFFF - end->counter_fpga)
+            + start->counter_fpga + 1)/divisor;
+    }
+    return time_elapsed;
+}
+
+uint64_t get_cycle_count_diff(base_time_counter *start,
+                              base_time_counter *end)
+{
+    if (start->counter_systick > end->counter_systick) {
+        warn("start > end; counter might have overflown\n");
+    }
+    return end->counter_systick - start->counter_systick;
+}
+
+void start_cycle_counter(void)
+{
+    /* Nothing to do for FPGA */
+}
+
+void stop_cycle_counter(void)
+{
+    /* Nothing to do for FPGA */
+}
+
+void SysTick_Handler(void)
+{
+    /* Increment the cycle counter based on load value. */
+    cpu_cycle_count += SysTick->LOAD + 1;
+}
+
+/**
+ * Gets the current SysTick derived counter value
+ */
+static uint64_t Get_SysTick_Cycle_Count(void)
+{
+    uint32_t systick_val;
+
+    NVIC_DisableIRQ(SysTick_IRQn);
+    systick_val = SysTick->VAL & SysTick_VAL_CURRENT_Msk;
+    NVIC_EnableIRQ(SysTick_IRQn);
+
+    return cpu_cycle_count + (SysTick->LOAD - systick_val);
+}
+
+
+/**
+ * SysTick initialisation
+ */
+static int Init_SysTick(void)
+{
+    const uint32_t ticks_10ms = get_mps3_core_clock()/100 + 1;
+    int err = 0;
+
+    /* Reset CPU cycle count value. */
+    cpu_cycle_count = 0;
+
+    /* Changing configuration for sys tick => guard from being
+     * interrupted. */
+    NVIC_DisableIRQ(SysTick_IRQn);
+
+    /* SysTick init - this will enable interrupt too. */
+    err = SysTick_Config(ticks_10ms);
+
+    /* Enable interrupt again. */
+    NVIC_EnableIRQ(SysTick_IRQn);
+
+    /* Wait for SysTick to kick off */
+    while (!err && !SysTick->VAL) {
+        __NOP();
+    }
+
+    return err;
+}
+
+uint32_t get_mps3_core_clock(void)
+{
+    const uint32_t default_clock = 32000000 /* 32 MHz clock */;
+    static int warned_once = 0;
+    if (0 != MPS3_SCC->CFG_ACLK) {
+        if (default_clock != MPS3_SCC->CFG_ACLK) {
+            warn("System clock is different to the MPS3 config set clock.\n");
+        }
+        return MPS3_SCC->CFG_ACLK;
+    }
+
+    if (!warned_once) {
+        warn("MPS3_SCC->CFG_ACLK reads 0. Assuming default clock of %" PRIu32 "\n",
+            default_clock);
+        warned_once = 1;
+    }
+    return default_clock;
+}
\ No newline at end of file