STCUBEMX code generation missing some pins?

[SYes.1]

So I'm new to the stm32 line up and I'm currently trying out the STCUBEMX code generator. After generating the code, I can't seem to find the configurations for the pins I selected. For example, I chose PD5 and PD6 as TX and RX for USART2. But when I check the auto-generated code, it doesn't seem to configure the gpio pins. It does set up USART2, but just not the pins. So does this mean that I'll have to set it up myself? If so, are there any examples I could reference from? Also, I'm not sure if I have to manually configure the pins myself for the auto-generated GPIO pins. For example, in line"107 shows "GPIO_InitStruct.Pin = SDIO1_CMD_Pin;". Do I have to edit SDIO1_CMD_Pin to configure it the pin SDIO1 is at (e.g.GPIO_PIN_??)? And what does HAL_GPIO_INIT() do? Do I call it once for every gpio A,B,C... Or do I have to call it every time I need to initiate a pin so for each PA pin I will have to call HAL_GPIO_INIT() each time?

static void MX_USART2_UART_Init(void)
{
 
  /* USER CODE BEGIN USART2_Init 0 */
 
  /* USER CODE END USART2_Init 0 */
 
  /* USER CODE BEGIN USART2_Init 1 */
 
  /* USER CODE END USART2_Init 1 */
  huart2.Instance = USART2;
  huart2.Init.BaudRate = 115200;
  huart2.Init.WordLength = UART_WORDLENGTH_8B;
  huart2.Init.StopBits = UART_STOPBITS_1;
  huart2.Init.Parity = UART_PARITY_NONE;
  huart2.Init.Mode = UART_MODE_TX_RX;
  huart2.Init.HwFlowCtl = UART_HWCONTROL_NONE;
  huart2.Init.OverSampling = UART_OVERSAMPLING_16;
  huart2.Init.OneBitSampling = UART_ONE_BIT_SAMPLE_DISABLE;
  huart2.Init.ClockPrescaler = UART_PRESCALER_DIV1;
  huart2.AdvancedInit.AdvFeatureInit = UART_ADVFEATURE_NO_INIT;
  if (HAL_UART_Init(&huart2) != HAL_OK)
  {
    Error_Handler();
  }
  if (HAL_UARTEx_SetTxFifoThreshold(&huart2, UART_TXFIFO_THRESHOLD_1_8) != HAL_OK)
  {
    Error_Handler();
  }
  if (HAL_UARTEx_SetRxFifoThreshold(&huart2, UART_RXFIFO_THRESHOLD_1_8) != HAL_OK)
  {
    Error_Handler();
  }
  if (HAL_UARTEx_DisableFifoMode(&huart2) != HAL_OK)
  {
    Error_Handler();
  }
  /* USER CODE BEGIN USART2_Init 2 */
 
  /* USER CODE END USART2_Init 2 */
 
}
 
static void MX_GPIO_Init(void)
{
  GPIO_InitTypeDef GPIO_InitStruct = {0};
 
  /* GPIO Ports Clock Enable */
  __HAL_RCC_GPIOI_CLK_ENABLE();
  __HAL_RCC_GPIOG_CLK_ENABLE();
  __HAL_RCC_GPIOK_CLK_ENABLE();
  __HAL_RCC_GPIOD_CLK_ENABLE();
  __HAL_RCC_GPIOC_CLK_ENABLE();
  __HAL_RCC_GPIOE_CLK_ENABLE();
  __HAL_RCC_GPIOB_CLK_ENABLE();
  __HAL_RCC_GPIOJ_CLK_ENABLE();
  __HAL_RCC_GPIOA_CLK_ENABLE();
  __HAL_RCC_GPIOF_CLK_ENABLE();
  __HAL_RCC_GPIOH_CLK_ENABLE();
 
  /*Configure GPIO pin Output Level */
  HAL_GPIO_WritePin(GPIOI, WIFI_BOOT_Pin|WIFI_WKUP_Pin|WIFI_RST_Pin, GPIO_PIN_RESET);
 
  /*Configure GPIO pin Output Level */
  HAL_GPIO_WritePin(GPIOG, USER_LED1_Pin|USER_LED2_Pin, GPIO_PIN_RESET);
 
  /*Configure GPIO pin Output Level */
  HAL_GPIO_WritePin(SPI2_NSS_GPIO_Port, SPI2_NSS_Pin, GPIO_PIN_RESET);
 
  /*Configure GPIO pin Output Level */
  HAL_GPIO_WritePin(AUDIO_NRST_GPIO_Port, AUDIO_NRST_Pin, GPIO_PIN_SET);
 
  /*Configure GPIO pin Output Level */
  HAL_GPIO_WritePin(GPIOA, LCD_BL_CTRL_Pin|LCD_ON_OFF_Pin, GPIO_PIN_SET);
 
  /*Configure GPIO pins : WIFI_GPIO_Pin WIFI_DATRDY_Pin */
  GPIO_InitStruct.Pin = WIFI_GPIO_Pin|WIFI_DATRDY_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_IT_RISING;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  HAL_GPIO_Init(GPIOI, &GPIO_InitStruct);
 
  /*Configure GPIO pins : SDIO1_D2_Pin SDIO1_CK_Pin SDIO1_D3_Pin SDIO1_D1_Pin
                           SDIO1_D0_Pin */
  GPIO_InitStruct.Pin = SDIO1_D2_Pin|SDIO1_CK_Pin|SDIO1_D3_Pin|SDIO1_D1_Pin
                          |SDIO1_D0_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_VERY_HIGH;
  GPIO_InitStruct.Alternate = GPIO_AF12_SDMMC1;
  HAL_GPIO_Init(GPIOC, &GPIO_InitStruct);
 
  /*Configure GPIO pins : WIFI_BOOT_Pin WIFI_WKUP_Pin WIFI_RST_Pin */
  GPIO_InitStruct.Pin = WIFI_BOOT_Pin|WIFI_WKUP_Pin|WIFI_RST_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(GPIOI, &GPIO_InitStruct);
 
  /*Configure GPIO pins : USER_LED1_Pin AUDIO_NRST_Pin USER_LED2_Pin */
  GPIO_InitStruct.Pin = USER_LED1_Pin|AUDIO_NRST_Pin|USER_LED2_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(GPIOG, &GPIO_InitStruct);
 
  /*Configure GPIO pin : SDIO1_CMD_Pin */
  GPIO_InitStruct.Pin = SDIO1_CMD_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_VERY_HIGH;
  GPIO_InitStruct.Alternate = GPIO_AF12_SDMMC1;
  HAL_GPIO_Init(SDIO1_CMD_GPIO_Port, &GPIO_InitStruct);
 
  /*Configure GPIO pin : uSD_Detect_Pin */
  GPIO_InitStruct.Pin = uSD_Detect_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_IT_RISING;
  GPIO_InitStruct.Pull = GPIO_PULLUP;
  HAL_GPIO_Init(uSD_Detect_GPIO_Port, &GPIO_InitStruct);
 
  /*Configure GPIO pin : SPI2_SCK_Pin */
  GPIO_InitStruct.Pin = SPI2_SCK_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  GPIO_InitStruct.Alternate = GPIO_AF5_SPI2;
  HAL_GPIO_Init(SPI2_SCK_GPIO_Port, &GPIO_InitStruct);
 
  /*Configure GPIO pins : SPI2_NSS_Pin LCD_BL_CTRL_Pin LCD_ON_OFF_Pin */
  GPIO_InitStruct.Pin = SPI2_NSS_Pin|LCD_BL_CTRL_Pin|LCD_ON_OFF_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(GPIOA, &GPIO_InitStruct);
 
 /*Configure GPIO pin : WAKEUP_Pin */
  GPIO_InitStruct.Pin = WAKEUP_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_IT_RISING;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  HAL_GPIO_Init(WAKEUP_GPIO_Port, &GPIO_InitStruct);
 
  /*Configure GPIO pin : MCO_Pin */
  GPIO_InitStruct.Pin = MCO_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  GPIO_InitStruct.Alternate = GPIO_AF0_MCO;
  HAL_GPIO_Init(MCO_GPIO_Port, &GPIO_InitStruct);
 
  /*Configure GPIO pins : SPI2_MISO_Pin SPI2_MOSI_Pin */
  GPIO_InitStruct.Pin = SPI2_MISO_Pin|SPI2_MOSI_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_AF_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  GPIO_InitStruct.Alternate = GPIO_AF5_SPI2;
  HAL_GPIO_Init(GPIOC, &GPIO_InitStruct);
 
  /*Configure GPIO pins : I2C4_SDA_Pin I2C4_SCL_Pin */
  GPIO_InitStruct.Pin = I2C4_SDA_Pin|I2C4_SCL_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_AF_OD;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  GPIO_InitStruct.Alternate = GPIO_AF4_I2C4;
  HAL_GPIO_Init(GPIOD, &GPIO_InitStruct);
 
  /*Configure GPIO pin : LCD_INT_Pin */
  GPIO_InitStruct.Pin = LCD_INT_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_IT_RISING;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  HAL_GPIO_Init(LCD_INT_GPIO_Port, &GPIO_InitStruct);
 
}

[TDK]

Pins for UART are initialized in stm32xxxx_hal_msp.c in HAL_UART_MspInit, which is called from HAL_UART_Init. It's similar for other peripherals.